def select_pseudos(pseudos, structure, ret_table=True):
"""
Given a list of pseudos and a pymatgen structure, extract the pseudopotentials
for the calculation (useful when we receive an entire periodic table).
Raises:
ValueError if no pseudo is found or multiple occurrences are found.
"""
table = PseudoTable.astable(pseudos)
pseudos = []
for symbol in structure.types_of_specie:
# Get the list of pseudopotentials in table from atom symbol.
pseudos_for_type = table.pseudos_with_symbol(symbol)
if not pseudos_for_type:
raise ValueError("Cannot find pseudo for symbol %s" % symbol)
if len(pseudos_for_type) > 1:
raise ValueError("Find multiple pseudos for symbol %s" % symbol)
pseudos.append(pseudos_for_type[0])
if ret_table:
return PseudoTable(pseudos)
else:
return pseudos
def num_valence_electrons(pseudos, structure):
"""
Compute the number of valence electrons from
a list of pseudopotentials and the crystalline structure.
Args:
pseudos:
List of strings, list of of pseudos or `PseudoTable` instance.
structure:
Pymatgen structure.
Raises:
ValueError if cannot find a pseudo in the input pseudos or if the
input list contains more than one pseudo for the chemical symbols
appearing in structure.
"""
table = PseudoTable.astable(pseudos)
valence = 0.0
for site in structure:
entries = table.pseudos_with_symbol(site.specie.symbol)
if len(entries) != 1:
raise ValueError("Found %d entries for symbol %s" %
(len(entries), site.specie.symbol))
valence += entries[0].Z_val
return valence
def select_pseudos(pseudos, structure, ret_table=True):
"""
Given a list of pseudos and a pymatgen structure, extract the pseudopotentials
for the calculation (useful when we receive an entire periodic table).
Raises:
ValueError if no pseudo is found or multiple occurrences are found.
"""
table = PseudoTable.astable(pseudos)
pseudos = []
for symbol in structure.types_of_specie:
# Get the list of pseudopotentials in table from atom symbol.
pseudos_for_type = table.pseudos_with_symbol(symbol)
if not pseudos_for_type:
raise ValueError("Cannot find pseudo for symbol %s" % symbol)
if len(pseudos_for_type) > 1:
raise ValueError("Find multiple pseudos for symbol %s" % symbol)
pseudos.append(pseudos_for_type[0])
if ret_table:
return PseudoTable(pseudos)
else:
return pseudos
def num_valence_electrons(pseudos, structure):
"""
Compute the number of valence electrons from
a list of pseudopotentials and the crystalline structure.
Args:
pseudos:
List of strings, list of of pseudos or `PseudoTable` instance.
structure:
Pymatgen structure.
Raises:
ValueError if cannot find a pseudo in the input pseudos or if the
input list contains more than one pseudo for the chemical symbols
appearing in structure.
"""
table = PseudoTable.astable(pseudos)
valence = 0.0
for site in structure:
entries = table.pseudos_with_symbol(site.specie.symbol)
if len(entries) != 1:
raise ValueError("Found %d entries for symbol %s" % (len(entries), site.specie.symbol))
valence += entries[0].Z_val
return valence
def calc_nvalence(self, pseudos):
"""
Returns the number of valence electrons.
Args:
pseudos:
List of `Pseudo` objects or list of pseudopotential filenames.
"""
table = PseudoTable.astable(pseudos)
nval = 0
for site in self:
symbol = site.species_string
pseudos = table.pseudos_with_symbol(symbol)
assert len(pseudos) == 1
nval += pseudos[0].Z_val
return nval
def select_pseudos(pseudos, structure):
"""
Given a list of pseudos and a pymatgen structure, extract the pseudopotentials
for the calculation (useful when we receive an entire periodic table).
Raises:
ValueError if no pseudo is found or multiple occurrences are found.
"""
table = PseudoTable.astable(pseudos)
pseudos = []
for typ in structure.types_of_specie:
# Get the list of pseudopotentials in table from atom symbol.
pseudos_for_type = table.pseudos_with_symbol(typ)
if pseudos_for_type is None or len(pseudos_for_type) != 1:
raise ValueError("Cannot find unique pseudo for type %s" % typ)
pseudos.append(pseudos_for_type[0])
return PseudoTable(pseudos)
