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Expose getting orbital params from name #251

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Expose getting orbital params from name #251

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1969310
enh: reading orbitals params from string as an static method
pfebrer Aug 8, 2020
67a2d05
maint: make sure tests pass for orbital
pfebrer Aug 8, 2020
46639d4
maint: some whitespaces
pfebrer Aug 8, 2020
c398802
maint: remove force_n from orbital name to params
pfebrer Aug 8, 2020
dee95f7
maint: checking if spherical orbital is None in the wrong place
pfebrer Aug 8, 2020
fef3904
maint: completed docs for orb_name_to_params
pfebrer Aug 8, 2020
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165 changes: 89 additions & 76 deletions sisl/orbital.py
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Original file line number Diff line number Diff line change
Expand Up @@ -773,68 +773,7 @@ def __init__(self, *args, **kwargs):
# String specification of the atomic orbital
s = args.pop(0)

_n = {'s': 1, 'p': 2, 'd': 3, 'f': 4, 'g': 5}
_l = {'s': 0, 'p': 1, 'd': 2, 'f': 3, 'g': 4}
_m = {'s': 0,
'pz': 0, 'px': 1, 'py': -1,
'dxy': -2, 'dyz': -1, 'dz2': 0, 'dxz': 1, 'dx2-y2': 2,
'fy(3x2-y2)': -3, 'fxyz': -2, 'fz2y': -1, 'fz3': 0,
'fz2x': 1, 'fz(x2-y2)': 2, 'fx(x2-3y2)': 3,
'gxy(x2-y2)': -4, 'gzy(3x2-y2)': -3, 'gz2xy': -2, 'gz3y': -1, 'gz4': 0,
'gz3x': 1, 'gz2(x2-y2)': 2, 'gzx(x2-3y2)': 3, 'gx4+y4': 4,
}

# First remove a P for polarization
P = 'P' in s
s = s.replace('P', '')

# Try and figure out the input
# 2s => n=2, l=0, m=0, z=1, P=False
# 2sZ2P => n=2, l=0, m=0, z=2, P=True
# 2pxZ2P => n=2, l=0, m=0, z=2, P=True
# By default a non-"n" specification takes the lowest value allowed
# s => n=1
# p => n=2
# ...
try:
n = int(s[0])
# Remove n specification
s = s[1:]
except:
n = _n.get(s[0])

# Get l
l = _l.get(s[0])

# Get number of zeta shell
iZ = s.find('Z')
if iZ >= 0:
# Currently we know that we are limited to 9 zeta shells.
# However, for now we assume this is enough (could easily
# be extended by a reg-exp)
try:
Z = int(s[iZ+1])
# Remove Z + int
s = s[:iZ] + s[iZ+2:]
except:
Z = 1
s = s[:iZ] + s[iZ+1:]

# We should be left with m specification
m = _m.get(s)

# Now we should figure out how the spherical orbital
# has been passed.
# There are two options:
# 1. The radial function is passed as two arrays: r, f
# 2. The SphericalOrbital-class is passed which already contains
# the relevant information.
# Figure out if it is a sphericalorbital
if len(args) > 0:
if isinstance(args[0], SphericalOrbital):
self.orb = args.pop(0)
else:
self.orb = SphericalOrbital(l, args.pop(0))
n, l, m, Z, P = self.orb_name_to_params(s, n=n, l=l, m=m, Z=Z, P=kwargs.get('P'))
else:

# Arguments *have* to be
Expand All @@ -858,13 +797,6 @@ def __init__(self, *args, **kwargs):
if isinstance(args[0], bool):
P = args.pop(0)

# Figure out if it is a sphericalorbital
if len(args) > 0:
if isinstance(args[0], SphericalOrbital):
self.orb = args.pop(0)
else:
self.orb = SphericalOrbital(l, args.pop(0))

# Still if n is None, we assign the default (lowest) quantum number
if n is None:
n = l + 1
Expand All @@ -881,15 +813,21 @@ def __init__(self, *args, **kwargs):
if abs(self.m) > self.l:
raise ValueError(self.__class__.__name__ + ' requires |m| <= l.')

# Retrieve user-passed spherical orbital
s = kwargs.get('spherical', None)

# Now we should figure out how the spherical orbital
# has been passed.
# There are two options:
# 1. The radial function is passed as two arrays: r, f
# 2. The SphericalOrbital-class is passed which already contains
# the relevant information.
# Figure out if it is a sphericalorbital
s = kwargs.get('spherical')
if s is None:
# Expect the orbital to already be set
pass
elif isinstance(s, Orbital):
if len(args) > 0:
s = args.pop(0)

if isinstance(s, SphericalOrbital):
self.orb = s
else:
elif s is not None:
self.orb = SphericalOrbital(l, s)

if self.orb is None:
Expand All @@ -899,6 +837,81 @@ def __init__(self, *args, **kwargs):

self.R = self.orb.R

@staticmethod
def orb_name_to_params(orb_name, n=None, l=None, m=None, Z=None, P=None):
"""
Gets the quantum numbers, Z shell and polarization corresponding to an orbital.

Parameters
------------
orb_name: str
the name for which we want to retreive the parameters
n: int, optional
the default value for n.
l: int, optional
the default value for n.
m: int, optional
the default value for n.
Z: int, optional
the default value for Z.
P: bool, optional
if provided, the value for P. Note that this is not the default, but will
be enforced.

Returns
--------
n, l, m, Z, P
"""

_l = {'s': 0, 'p': 1, 'd': 2, 'f': 3, 'g': 4}
_m = {'s': 0,
'pz': 0, 'px': 1, 'py': -1,
'dxy': -2, 'dyz': -1, 'dz2': 0, 'dxz': 1, 'dx2-y2': 2,
'fy(3x2-y2)': -3, 'fxyz': -2, 'fz2y': -1, 'fz3': 0,
'fz2x': 1, 'fz(x2-y2)': 2, 'fx(x2-3y2)': 3,
'gxy(x2-y2)': -4, 'gzy(3x2-y2)': -3, 'gz2xy': -2, 'gz3y': -1, 'gz4': 0,
'gz3x': 1, 'gz2(x2-y2)': 2, 'gzx(x2-3y2)': 3, 'gx4+y4': 4,
}

if P is None:
# First remove a P for polarization
P = 'P' in orb_name
orb_name = orb_name.replace('P', '')

# Try and figure out the input
# 2s => n=2, l=0, m=0, z=1, P=False
# 2sZ2P => n=2, l=0, m=0, z=2, P=True
# 2pxZ2P => n=2, l=0, m=0, z=2, P=True
try:
n = int(orb_name[0])
# Remove n specification
orb_name = orb_name[1:]
except:
pass

if orb_name:
# Get l
l = _l.get(orb_name[0], l)

# Get number of zeta shell
iZ = orb_name.find('Z')
if iZ >= 0:
# Currently we know that we are limited to 9 zeta shells.
# However, for now we assume this is enough (could easily
# be extended by a reg-exp)
try:
Z = int(orb_name[iZ+1])
# Remove Z + int
orb_name = orb_name[:iZ] + orb_name[iZ+2:]
except:
Z = 1
orb_name = orb_name[:iZ] + orb_name[iZ+1:]

# We should be left with m specification
m = _m.get(orb_name, m)

return n, l, m, Z, P

@property
def f(self):
return self.orb.f
Expand Down
3 changes: 3 additions & 0 deletions sisl/tests/test_orbital.py
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Original file line number Diff line number Diff line change
Expand Up @@ -287,6 +287,9 @@ def test_init1(self):
a.append(AtomicOrbital('pzP', f))
a.append(AtomicOrbital('pzP', rf))
a.append(AtomicOrbital('2pzP', rf))
a.append(AtomicOrbital('2', rf, l=1, m=0, Z=1, P=True))
a.append(AtomicOrbital('2p', m=0, Z=1, P=True, spherical=f))
a.append(AtomicOrbital('2p', "dummy", m=0, Z=1, P=True, spherical=rf))
for i in range(len(a) - 1):
for j in range(i+1, len(a)):
assert a[i] == a[j] and a[i].equal(a[j], psi=True, radial=True)
Expand Down