def IP_EA(symb, remove_orb, add_orb, remove, add, add_args={}):
""" Return ionization potential and electron affinity for given atom,
and the valence energies of neutral atom.
parameters:
-----------
symb: element symbol
remove_orb: orbital from where to remove atoms (e.g. '2p')
add_orb: orbital from where to add atoms (e.g. '2p')
remove: how many electrons to remove
add: how many electrons to add
(remove and add can be different from 1.0 if DFT should not
be stable to e.g. adding one full electron)
Fit second order curve for 3 points and return IP and EA for full
electron adding and removal.
"""
#from box.data import atom_occupations
atom = KSAllElectron(symb, txt='-', **add_args)
# add electrons -> negative ion
#occu=atom_occupations[symb].copy()
w = 'negative.atom'
occu_add = atom.occu.copy()
occu_add[add_orb] += add
ea = KSAllElectron(symb,
configuration=occu_add,
restart=w,
write=w,
**add_args)
ea.run()
# neutral atom
w = 'neutral.atom'
neutral = KSAllElectron(symb, restart=w, write=w, **add_args)
neutral.run()
valence_energies = neutral.get_valence_energies()
# remove electrons -> positive ion
#occu=atom_occupations[symb].copy()
w = 'positive.atom'
occu_remove = atom.occu.copy()
occu_remove[remove_orb] -= remove
ip = KSAllElectron(symb,
configuration=occu_remove,
restart=w,
write=w,
**add_args)
ip.run()
e0 = neutral.get_energy()
en = ea.get_energy() - e0
ep = ip.get_energy() - e0
# e(x)=e0+c1*x+c2*x**2 =energy as a function of additional electrons
c2 = (en + ep * add / remove) / (add * (remove + add))
c1 = (c2 * remove**2 - ep) / remove
IP = -c1 + c2
EA = -(c1 + c2)
return IP, EA, neutral
def IP_EA(symb,remove_orb,add_orb,remove,add,add_args={}):
""" Return ionization potential and electron affinity for given atom,
and the valence energies of neutral atom.
parameters:
-----------
symb: element symbol
remove_orb: orbital from where to remove atoms (e.g. '2p')
add_orb: orbital from where to add atoms (e.g. '2p')
remove: how many electrons to remove
add: how many electrons to add
(remove and add can be different from 1.0 if DFT should not
be stable to e.g. adding one full electron)
Fit second order curve for 3 points and return IP and EA for full
electron adding and removal.
"""
#from box.data import atom_occupations
atom = KSAllElectron(symb, txt='-', **add_args)
# add electrons -> negative ion
#occu=atom_occupations[symb].copy()
w = 'negative.atom'
occu_add = atom.occu.copy()
occu_add[add_orb] += add
ea = KSAllElectron(symb, configuration=occu_add, restart=w, write=w,
**add_args)
ea.run()
# neutral atom
w = 'neutral.atom'
neutral = KSAllElectron(symb, restart=w, write=w, **add_args)
neutral.run()
valence_energies = neutral.get_valence_energies()
# remove electrons -> positive ion
#occu=atom_occupations[symb].copy()
w = 'positive.atom'
occu_remove = atom.occu.copy()
occu_remove[remove_orb] -= remove
ip = KSAllElectron(symb, configuration=occu_remove, restart=w, write=w,
**add_args)
ip.run()
e0 = neutral.get_energy()
en = ea.get_energy()-e0
ep = ip.get_energy()-e0
# e(x)=e0+c1*x+c2*x**2 =energy as a function of additional electrons
c2 = (en+ep*add/remove)/(add*(remove+add))
c1 = (c2*remove**2-ep)/remove
IP = -c1+c2
EA = -(c1+c2)
return IP, EA, neutral
def electron_affinity(symb, add, electrons=1.0):
""" Return electron affinity of given atom.
parameters:
-----------
symb: element symbol
add: orbital where electron is added (e.g. '2p')
electrons: how many electrons are added. Can be fractional number
if DFT should not be stable. EA is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu = atom_occupations[symb].copy()
# neutral atom
atom = KSAllElectron(symb)
atom.run()
e0 = atom.get_energy()
# positive ion
occu[add] += electrons
ion = KSAllElectron(symb, occu=occu)
ion.run()
e1 = ion.get_energy()
return (e0 - e1) / electrons
def electron_affinity(symb,add,electrons=1.0):
""" Return electron affinity of given atom.
parameters:
-----------
symb: element symbol
add: orbital where electron is added (e.g. '2p')
electrons: how many electrons are added. Can be fractional number
if DFT should not be stable. EA is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu=atom_occupations[symb].copy()
# neutral atom
atom=KSAllElectron(symb)
atom.run()
e0=atom.get_energy()
# positive ion
occu[add]+=electrons
ion=KSAllElectron(symb,occu=occu)
ion.run()
e1=ion.get_energy()
return (e0-e1)/electrons
def ionization_potential(symb, remove, electrons=1.0):
""" Return ionization potential of given atom.
parameters:
-----------
symb: element symbol
remove: orbital from where electron is removed (e.g. '2p')
electrons: how many electrons to remove. Can be fractional number
if DFT should not be stable. IP is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu = atom_occupations[symb].copy()
# neutral atom
atom = KSAllElectron(symb)
atom.run()
e0 = atom.get_energy()
# negative ion
occu[remove] -= electrons
ion = KSAllElectron(symb, occu=occu)
ion.run()
e1 = ion.get_energy()
return (e1 - e0) / electrons
def ionization_potential(symb,remove,electrons=1.0):
""" Return ionization potential of given atom.
parameters:
-----------
symb: element symbol
remove: orbital from where electron is removed (e.g. '2p')
electrons: how many electrons to remove. Can be fractional number
if DFT should not be stable. IP is scaled by
electrons^-1 in the end to extrapolate to electrons=1.
"""
from box.data import atom_occupations
occu=atom_occupations[symb].copy()
# neutral atom
atom=KSAllElectron(symb)
atom.run()
e0=atom.get_energy()
# negative ion
occu[remove]-=electrons
ion=KSAllElectron(symb,occu=occu)
ion.run()
e1=ion.get_energy()
return (e1-e0)/electrons