def setUp(self):
self.pbe_db = df_database(XcFunc.from_name("PBE"))
assert self.pbe_db.xc == "PBE"
# Cached?
assert df_database(XcFunc.from_abinit_ixc(11)) is self.pbe_db
assert "WIEN2k" in self.pbe_db.codes
assert "VASP" in self.pbe_db.codes
spinat, spin_mode = self.pbe_db.spinat_spinmode_for_symbol("Si")
assert spinat is None and spin_mode == "unpolarized"
spinat, spin_mode = self.pbe_db.spinat_spinmode_for_symbol("Fe")
assert spinat == 2 * [(0, 0, 2.3)] and spin_mode == "polarized"
self.pw_db = df_database("PW")
assert self.pw_db.xc == "PW"
assert self.pw_db is not self.pbe_db
assert "WIEN2k" in self.pw_db.codes
# Accept PW_MOD as well.
self.pwmod_db = df_database("PW_MOD")
assert self.pwmod_db.xc == "PW_MOD"
assert self.pwmod_db is not self.pw_db
def setUp(self):
self.pbe_db = df_database(XcFunc.from_name("PBE"))
assert self.pbe_db.xc == "PBE"
# Cached?
assert df_database(XcFunc.from_abinit_ixc(11)) is self.pbe_db
assert "WIEN2k" in self.pbe_db.codes
assert "VASP" in self.pbe_db.codes
spinat, spin_mode = self.pbe_db.spinat_spinmode_for_symbol("Si")
assert spinat is None and spin_mode == "unpolarized"
spinat, spin_mode = self.pbe_db.spinat_spinmode_for_symbol("Fe")
assert spinat == 2 * [(0, 0, 2.3)] and spin_mode == "polarized"
self.pw_db = df_database("PW")
assert self.pw_db.xc == "PW"
assert self.pw_db is not self.pbe_db
assert "WIEN2k" in self.pw_db.codes
# Accept PW_MOD as well.
self.pwmod_db = df_database("PW_MOD")
assert self.pwmod_db.xc == "PW_MOD"
assert self.pwmod_db is not self.pw_db
class DojoInfo(AttrDict):
"""
Dictionary with metadata associated to the PseudoDojo table.
"""
# See https://github.com/Julian/jsonschema
JSON_SCHEMA = {
"$schema": "http://json-schema.org/schema#",
"type": "object",
"properties": {
"pp_type": {"type": "string", "enum": ["NC", "PAW"]},
"xc_name": {"type": "string", "enum": XcFunc.aliases()},
"authors": {"type": "array"},
"description": {"type": "string"},
"references": {"type": "array"},
"dojo_dir": {"type": "string"},
#"generation_date": {"type": "string", "format": "date"},
#"tags": {"type": "array", "items": {"type": "string", "enum": ["accuracy", "efficiency"]}},
#"relativity": {"type": "string", "enum": ["non-relativistic", "scalar-relativistic", "relativistic"]}
},
"required": ["pp_type", "xc_name", "authors", "description", "references", "dojo_dir",
#"generation_date", "tags", "relativity"
],
}
def __init__(self, *args, **kwargs):
super(DojoInfo, self).__init__(*args, **kwargs)
self["xc"] = XcFunc.from_name(self["xc_name"])
def validate_json_schema(self):
"""Validate DojoInfo with validictory."""
from jsonschema import validate
validate(self, self.JSON_SCHEMA)
@classmethod
def get_template_dict(cls):
"""Return a dictionary with the keys that must be filled by the user."""
return {k: str(v) for k, v in cls.JSON_SCHEMA["properties"].items()}
@property
def isnc(self):
"""True if norm-conserving pseudopotential."""
return self.pp_type == "NC"
@property
def ispaw(self):
"""True if PAW pseudopotential."""
return self.pp_type == "PAW"
def __init__(self, xc):
"""
Read data from CSV files and initialize the object.
xc specifies the XC functionals used.
"""
self.xc = XcFunc.asxc(xc)
if self.xc != "PBE":
raise ValueError("Gbrv database supports only PBE pseudos")
# Directory containing the GBRV tables in CSV format.
datadir = os.path.abspath(os.path.dirname(__file__))
datadir = os.path.join(datadir, "data")
# Build dictionary of tables.
self.tables = tables = {}
for stype in self.all_struct_types:
filepath = os.path.join(datadir, stype + ".csv")
tables[stype] = read_table_from_file(filepath)
def __init__(self, xc):
"""
Read data from CSV files and initialize the object.
xc specifies the XC functionals used.
"""
self.xc = XcFunc.asxc(xc)
if self.xc != "PBE":
raise ValueError("Gbrv database supports only PBE pseudos")
# Directory containing the GBRV tables in CSV format.
datadir = os.path.abspath(os.path.dirname(__file__))
datadir = os.path.join(datadir, "data")
# Build dictionary of tables.
self.tables = tables = {}
for stype in self.all_struct_types:
filepath = os.path.join(datadir, stype + ".csv")
tables[stype] = read_table_from_file(filepath)
def __init__(self, xc):
""""xc specifies the XC functionals used."""
self.xc = XcFunc.asxc(xc)
dirpath = os.path.abspath(os.path.dirname(__file__))
self.dirpath = os.path.join(dirpath, "data")
self._data = {}
for bname in self._FILES4XC[self.xc]:
file_path = os.path.join(self.dirpath, bname)
if os.path.isfile(file_path) and file_path.endswith(".txt"):
code, ext = os.path.splitext(bname)
code = code.split("-")[0]
self._data[code] = read_data_from_filepath(file_path, self.xc)
self._cif_paths = {}
#loc = "CIFs" + "-" + str(self.xc)
loc = self._CIFDIR4XC[self.xc]
cif_dirpath = os.path.join(self.dirpath, loc)
for bname in os.listdir(cif_dirpath):
if bname.endswith(".cif"):
symbol, ext = os.path.splitext(bname)
self._cif_paths[symbol] = os.path.join(cif_dirpath, bname)
def __init__(self, xc):
""""xc specifies the XC functionals used."""
self.xc = XcFunc.asxc(xc)
dirpath = os.path.abspath(os.path.dirname(__file__))
self.dirpath = os.path.join(dirpath, "data")
self._data = {}
for bname in self._FILES4XC[self.xc]:
file_path = os.path.join(self.dirpath, bname)
if os.path.isfile(file_path) and file_path.endswith(".txt"):
code, ext = os.path.splitext(bname)
code = code.split("-")[0]
self._data[code] = read_data_from_filepath(file_path, self.xc)
self._cif_paths = {}
#loc = "CIFs" + "-" + str(self.xc)
loc = self._CIFDIR4XC[self.xc]
cif_dirpath = os.path.join(self.dirpath, loc)
for bname in os.listdir(cif_dirpath):
if bname.endswith(".cif"):
symbol, ext = os.path.splitext(bname)
self._cif_paths[symbol] = os.path.join(cif_dirpath, bname)
def __init__(self, *args, **kwargs):
super(DojoInfo, self).__init__(*args, **kwargs)
self["xc"] = XcFunc.from_name(self["xc_name"])
def __init__(self, *args, **kwargs):
super(DojoInfo, self).__init__(*args, **kwargs)
self["xc"] = XcFunc.from_name(self["xc_name"])
def test_xcfunc_api(self):
"""Testing XcFunc API."""
# Aliases should be unique
assert len(XcFunc.aliases()) == len(set(XcFunc.aliases()))
# LDA-Teter
ixc_1 = XcFunc.from_abinit_ixc(1)
print(ixc_1)
assert ixc_1.type == "LDA"
assert ixc_1.name == "LDA_XC_TETER93"
assert ixc_1 == ixc_1
assert ixc_1 == "LDA_XC_TETER93"
assert ixc_1 != "PBE"
assert ixc_1.name not in XcFunc.aliases()
assert ixc_1 == XcFunc.from_name(ixc_1.name)
# LDA-PW (in aliases)
ixc_7 = XcFunc.from_abinit_ixc(7)
assert ixc_7.type == "LDA"
assert ixc_7.name == "PW"
assert ixc_7.name in XcFunc.aliases()
assert ixc_7.name == XcFunc.from_name(ixc_7.name)
assert ixc_7 != ixc_1
# GGA-PBE from ixc == 11 (in aliases)
ixc_11 = XcFunc.from_abinit_ixc(11)
assert ixc_11.type == "GGA" and ixc_11.name == "PBE"
assert ixc_11.name in XcFunc.aliases()
assert ixc_1 != ixc_11
# Test asxc
assert XcFunc.asxc(ixc_11) is ixc_11
assert XcFunc.asxc("PBE") == ixc_11
d = {ixc_11: ixc_11.name}
print(d)
assert "PBE" in d
assert ixc_11 in d
# Test if object can be serialized with Pickle.
self.serialize_with_pickle(ixc_11, test_eq=True)
# Test if object supports MSONable
# TODO
# print("in test", type(ixc_11.x), type(ixc_11.c), type(ixc_11.xc))
# ixc_11.x.as_dict()
# self.assertMSONable(ixc_11)
# GGA-PBE from ixc given in abinit-libxc mode
ixc_101130 = XcFunc.from_abinit_ixc(-101130)
assert ixc_101130.type == "GGA" and ixc_101130.name == "PBE"
assert ixc_101130 == ixc_11
# GGA-PBE built from name
gga_pbe = XcFunc.from_name("PBE")
assert gga_pbe.type == "GGA" and gga_pbe.name == "PBE"
assert ixc_11 == gga_pbe
# Use X from GGA and C from LDA!
unknown_xc = XcFunc.from_name("GGA_X_PBE+ LDA_C_PW")
assert unknown_xc not in XcFunc.aliases()
assert unknown_xc.type == "GGA+LDA"
assert unknown_xc.name == "GGA_X_PBE+LDA_C_PW"
gga_pbe = XcFunc.from_type_name("GGA", "GGA_X_PBE+GGA_C_PBE")
assert gga_pbe.type == "GGA" and gga_pbe.name == "PBE"
assert str(gga_pbe) == "PBE"
def read_abinit_xcfunc(self):
"""
Read ixc from an Abinit file. Return :class:`XcFunc` object.
"""
ixc = int(self.read_value("ixc"))
return XcFunc.from_abinit_ixc(ixc)
def test_gbrv(self):
"""Testing GBRV database..."""
# Init the database.
db = gbrv_database(xc="PBE")
assert db.xc == "PBE"
# Cached?
assert gbrv_database(XcFunc.from_abinit_ixc(11)) is db
# Test basic methods
assert db.has_symbol("Si", stype="fcc")
assert not db.has_symbol("Si", stype="rocksalt")
assert "KMgF3" in db.all_symbols
db.print_formulas()
with self.assertRaises(ValueError):
gbrv_database(xc="PW")
# Get FCC entry for Silicon
fcc_si = db.get_fcc_entry("Si")
assert fcc_si.ae == 3.857 and fcc_si.gbrv_uspp == 3.853
assert fcc_si.struct_type == "fcc" and fcc_si.species == ["Si"]
sfcc = fcc_si.build_structure()
self.assert_almost_equal(sfcc.volume, fcc_si.ae**3 /4.)
# Get BCC entry for H
bcc_h = db.get_bcc_entry("H")
assert bcc_h.ae == 1.806 and bcc_h.gbrv_paw == 1.807
assert bcc_h.struct_type == "bcc" and bcc_h.species == ["H"]
sbcc = bcc_h.build_structure()
self.assert_almost_equal(sbcc.volume, bcc_h.ae**3 /2.)
# Hg is missing.
missing = db.get_bcc_entry("Hg")
assert missing.ae is None
# Get Rocksalt entry for LiF
lif = db.get_rocksalt_entry("LiF")
assert lif.symbol == "LiF" and lif.struct_type == "rocksalt"
assert lif.species == ["Li", "F"]
assert lif.ae == 4.076 and lif.pslib == 4.081
struct = lif.build_structure()
#print(struct.to_abivars())
# Get AB03 entry for SrLiF3
srlif3 = db.get_abo3_entry("SrLiF3")
assert srlif3.symbol == "SrLiF3" and srlif3.struct_type == "ABO3"
assert srlif3.ae == 3.884 and srlif3.gbrv_paw == 3.883
# TODO
#srlif3.build_structure()
# Get hH entry for SrLiF3
agalge = db.get_hH_entry("AgAlGe")
assert agalge.symbol == "AgAlGe" and agalge.struct_type == "hH"
assert agalge.ae == 6.224 and agalge.gbrv_paw == 6.218
# TODO
#agalge.build_structure()
assert len(db.entries_with_symbol("Si")) == 10
assert not db.entries_with_symbol("Lu")
assert db.match_symbols(["Si", "Lu"]) is None
assert db.match_symbols(["Si", "O"]).formula == "SiO"
e = db.entries_with_symbols(["Sr", "Si", "O"])
assert e and len(e) == 1 and e[0].formula == "SrSiO3"
def read_abinit_xcfunc(self):
"""
Read ixc from an Abinit file. Return :class:`XcFunc` object.
"""
ixc = int(self.read_value("ixc"))
return XcFunc.from_abinit_ixc(ixc)
def __init__(self, xc):
"""xc is the exchange-correlation functional e.g. PBE, PW."""
self.xc = XcFunc.asxc(xc)
def test_xcfunc_api(self):
"""Testing XcFunc API."""
# Aliases should be unique
assert len(XcFunc.aliases()) == len(set(XcFunc.aliases()))
# LDA-Teter
ixc_1 = XcFunc.from_abinit_ixc(1)
print(ixc_1)
assert ixc_1.type == "LDA"
assert ixc_1.name == "LDA_XC_TETER93"
assert ixc_1 == ixc_1
assert ixc_1 == "LDA_XC_TETER93"
assert ixc_1 != "PBE"
assert ixc_1.name not in XcFunc.aliases()
assert ixc_1 == XcFunc.from_name(ixc_1.name)
# LDA-PW (in aliases)
ixc_7 = XcFunc.from_abinit_ixc(7)
assert ixc_7.type == "LDA"
assert ixc_7.name == "PW"
assert ixc_7.name in XcFunc.aliases()
assert ixc_7.name == XcFunc.from_name(ixc_7.name)
assert ixc_7 != ixc_1
# GGA-PBE from ixc == 11 (in aliases)
ixc_11 = XcFunc.from_abinit_ixc(11)
assert ixc_11.type == "GGA" and ixc_11.name == "PBE"
assert ixc_11.name in XcFunc.aliases()
assert ixc_1 != ixc_11
# Test asxc
assert XcFunc.asxc(ixc_11) is ixc_11
assert XcFunc.asxc("PBE") == ixc_11
d = {ixc_11: ixc_11.name}
print(d)
assert "PBE" in d
assert ixc_11 in d
# Test if object can be serialized with Pickle.
self.serialize_with_pickle(ixc_11, test_eq=True)
# Test if object supports MSONable
# TODO
#print("in test", type(ixc_11.x), type(ixc_11.c), type(ixc_11.xc))
#ixc_11.x.as_dict()
#self.assertMSONable(ixc_11)
# GGA-PBE from ixc given in abinit-libxc mode
ixc_101130 = XcFunc.from_abinit_ixc(-101130)
assert ixc_101130.type == "GGA" and ixc_101130.name == "PBE"
assert ixc_101130 == ixc_11
# GGA-PBE built from name
gga_pbe = XcFunc.from_name("PBE")
assert gga_pbe.type == "GGA" and gga_pbe.name == "PBE"
assert ixc_11 == gga_pbe
# Use X from GGA and C from LDA!
unknown_xc = XcFunc.from_name("GGA_X_PBE+ LDA_C_PW")
assert unknown_xc not in XcFunc.aliases()
assert unknown_xc.type == "GGA+LDA"
assert unknown_xc.name == "GGA_X_PBE+LDA_C_PW"
