def __init__(self, name):
self.raw = name
# element symbol and atomic weight
if name == "p":
self.el = "H"
self.A = 1
elif name == "d":
self.el = "H"
self.A = 2
elif name == "t":
self.el = "H"
self.A = 3
elif name == "n":
self.el = "n"
self.A = 1
else:
e = re.match("([a-zA-Z]*)(\d*)", name)
self.el = e.group(1).title() # chemical symbol
self.A = int(e.group(2))
# atomic number comes from periodtable
i = elements.isotope("{}-{}".format(self.A, self.el))
self.Z = i.number
self.N = self.A - self.Z
# latex formatted style
self.pretty = r"{{}}^{{{}}}\mathrm{{{}}}".format(self.A, self.el)
def molecule_mass(M: str, as_amu=False) -> float:
atoms = M.split(" ")
m = 0
for ai in atoms:
match = re.match(r'([0-9]*)([A-Z][a-z]?)([0-9]*)', ai)
if match is None:
raise Exception(f"Invalid atom '{ai}'")
element = elements.isotope(match.group(2))
if match.group(1) == "":
mi = element.mass
else:
mi = element[int(match.group(1))].mass
m += mi*(int(match.group(3)) if match.group(3) != "" else 1)
return m if as_amu else m*amu2kg
def atomic_mass(atom_symbol, isotope=''):
"""atomic mass for atom_symbol, return most abundant atomic mass
if isotope not given.
"""
elem = elements.isotope(atom_symbol)
if isotope != '':
mass = elem[int(isotope)].mass # have isotopic mass
else:
# most abundant isotopic mass
elem_abund = []
for iso in elem.isotopes:
elem_abund.append(elem[iso].abundance)
elem_abund = np.asarray(elem_abund)
mass = elem[elem.isotopes[elem_abund.argmax()]].mass
return mass
def test():
# Check that we can access element properties
assert H.name == "hydrogen"
assert H.symbol == "H"
assert H.number == 1
assert helium.symbol == 'He'
# Check that isotopes work and produce the correct strings and symbols
O.add_isotope(18)
assert H[2].symbol == 'D'
assert H[3].symbol == 'T'
assert O[18].symbol == 'O'
assert str(H[2]) == 'D'
assert str(H[3]) == 'T'
assert str(O[18]) == '18-O'
try:
Fe[12]
except KeyError as msg:
assert msg.args[0] == '12 is not an isotope of Fe'
# Check that "for el in elements" works and for iso in el works
els = tuple(el for el in elements)
assert els[0].number == 0
assert els[1].number == 1
isotopes = tuple(iso for iso in O)
assert isotopes[0].isotope == 12 # 12 is the first oxygen isotope listed
# Check that table lookup works and fails appropriately
Fe.add_isotope(56)
assert elements.symbol('Fe') == Fe
assert elements.name('iron') == Fe
assert elements.isotope('Fe') == Fe
assert elements.isotope('56-Fe') == Fe[56]
assert elements.isotope('D') == H[2]
try:
elements.symbol('Qu')
except ValueError as msg:
assert str(msg) == "unknown element Qu"
try:
elements.name('Qu')
except ValueError as msg:
assert str(msg) == "unknown element Qu"
try:
elements.isotope('Qu')
except ValueError as msg:
assert str(msg) == "unknown element Qu"
try:
elements.isotope('4-D')
except ValueError as msg:
assert str(msg) == "unknown element 4-D"
# Check that ions work
assert Fe.ion[2].charge == 2
assert Fe.ions == (-4, -2, -1, 1, 2, 3, 4, 5, 6, 7)
assert str(Fe.ion[2]) == "Fe{2+}"
assert str(O.ion[-2]) == "O{2-}"
try:
Fe.ion[-3]
raise Exception("accepts invalid ions")
except ValueError as msg:
assert str(msg) == "-3 is not a valid charge for Fe"
assert data_files()[0][0] == "periodictable-data/xsf"
Fe[12]
except KeyError,msg:
assert msg.args[0] == '12 is not an isotope of Fe'
# Check that "for el in elements" works and for iso in el works
els = tuple(el for el in elements)
assert els[0].number == 0
assert els[1].number == 1
isotopes = tuple(iso for iso in O)
assert isotopes[0].isotope == 12 # 12 is the first oxygen isotope listed
# Check that table lookup works and fails appropriately
Fe.add_isotope(56)
assert elements.symbol('Fe') == Fe
assert elements.name('iron') == Fe
assert elements.isotope('Fe') == Fe
assert elements.isotope('56-Fe') == Fe[56]
assert elements.isotope('D') == H[2]
try:
elements.symbol('Qu')
except ValueError,msg:
assert str(msg) == "unknown element Qu"
try:
elements.name('Qu')
except ValueError,msg:
assert str(msg) == "unknown element Qu"
try:
elements.isotope('Qu')
except ValueError,msg:
assert str(msg) == "unknown element Qu"
try:
def test():
# Check that we can access element properties
assert H.name == "hydrogen"
assert H.symbol == "H"
assert H.number == 1
assert helium.symbol == 'He'
# Check that isotopes work and produce the correct strings and symbols
O.add_isotope(18)
assert H[2].symbol == 'D'
assert H[3].symbol == 'T'
assert O[18].symbol == 'O'
assert str(H[2]) == 'D'
assert str(H[3]) == 'T'
assert str(O[18]) == '18-O'
try:
Fe[12]
except KeyError as msg:
assert msg.args[0] == '12 is not an isotope of Fe'
# Check that "for el in elements" works and for iso in el works
els = tuple(el for el in elements)
assert els[0].number == 0
assert els[1].number == 1
isotopes = tuple(iso for iso in O)
assert isotopes[0].isotope == 12 # 12 is the first oxygen isotope listed
# Check that table lookup works and fails appropriately
Fe.add_isotope(56)
assert elements.symbol('Fe') == Fe
assert elements.name('iron') == Fe
assert elements.isotope('Fe') == Fe
assert elements.isotope('56-Fe') == Fe[56]
assert elements.isotope('D') == H[2]
try:
elements.symbol('Qu')
except ValueError as msg:
assert str(msg) == "unknown element Qu"
try:
elements.name('Qu')
except ValueError as msg:
assert str(msg) == "unknown element Qu"
try:
elements.isotope('Qu')
except ValueError as msg:
assert str(msg) == "unknown element Qu"
try:
elements.isotope('4-D')
except ValueError as msg:
assert str(msg) == "unknown element 4-D"
# Check that ions work
assert Fe.ion[2].charge == 2
assert Fe.ions == (2, 3)
assert str(Fe.ion[2]) == "Fe{2+}"
assert str(O.ion[-2]) == "O{2-}"
try:
Fe.ion[1]
raise Exception("accepts invalid ions")
except ValueError as msg:
assert str(msg) == "1 is not a valid charge for Fe"
assert data_files()[0][0] == "periodictable-data/xsf"
