def biatomic(atoms, A, B, R1=3.0, calc_energy=False):
r"""This routine analyzes atomic structure
by the calculation of coordination numbers
in cluster with atoms of two types (A and B).
Parameters
----------
atoms: ase.Atoms
ase Atoms object, containing atomic cluster.
A: string
atom type, like 'Ag', 'Pt', etc.
B: string
atom type, like 'Ag', 'Pt', etc.
R1: float
First coordination shell will icnlude all atoms
with distance less then R1 [Angstrom].
Default value is 3.
calc_energy: bool
Flag used for calculation of potential energy with EMT
calculator. The default value is False, so that
energy is not calculated.
Returns
-------
N: int
number of atoms in cluster
nA:
number of atoms of type A
R: float
radius of the cluster
CN_AA: float
average number of atoms A around atom A
CN_AB: float
average number of atoms A around atom B
CN_BB: float
average number of atoms B around atom B
CN_BA: float
average number of atoms B around atom A
etha: float
parameter of local ordering, -1 < etha < 1.
Returns 999 if concentration of one of the
component is too low.
E: float
potential energy
NAcore:
number of A atoms in core
NBcore:
number of B atoms in core
CNshellAA:
average CN of A-A for surface atoms only
CNshellAB:
average CN of A-B for surface atoms only
CNshellBB:
average CN of B-B for surface atoms only
CNshellBA:
average CN of B-A for surface atoms only
Notes
-----
The radius of the cluster is roughly determined as
maximum the distance from the center to most distant atom
in the cluster.
Example
--------
>>> atoms = FaceCenteredCubic('Ag',
[(1, 0, 0), (1, 1, 0), (1, 1, 1)], [7,8,7], 4.09)
>>> atoms = CoreShellFCC(atoms, 'Pt', 'Ag', 0.6, 4.09)
>>> [N, nA, R, CN_AA, CN_AB, CN_BB, CN_BA, etha] =
biatomic(atoms, 'Pt', 'Ag')
>>> print "Short range order parameter: ", etha
"""
N = len(atoms)
nA = 0
nB = 0
for element in atoms.get_chemical_symbols():
if element == A:
nA += 1
elif element == B:
nB += 1
else:
raise Exception('Extra element ' + element)
if (nA + nB != N):
raise Exception('Number of A (' + str(nA) + ') ' +
'and B (' + str(nB) + ') artoms mismatch!')
nl = NeighborList([R1 / 2.0] * N, self_interaction=False, bothways=True)
nl.build(atoms)
# initialize counters:
CN_AA = 0 # averaged total coord. numbers
CN_AB = 0
CN_BB = 0
CN_BA = 0
NAcore = 0 # number of atoms in core region
NBcore = 0
CNshellAA = 0 # average coord. numbers for surface atoms
CNshellAB = 0
CNshellBB = 0
CNshellBA = 0
for iatom in xrange(0, N):
indeces, offsets = nl.get_neighbors(iatom)
if atoms[iatom].symbol == B:
CN_BB_temp = 0
CN_BA_temp = 0
for ii in indeces:
if atoms[ii].symbol == B:
CN_BB_temp += 1
else: # atoms[i].symbol == A :
CN_BA_temp += 1
CN_BB += CN_BB_temp
CN_BA += CN_BA_temp
if len(indeces) < 12:
# SHELL
CNshellBB += CN_BB_temp
CNshellBA += CN_BA_temp
else:
# CORE
NBcore += 1
else: # atoms[iatom].symbol == A :
CN_AA_temp = 0
CN_AB_temp = 0
for i in indeces:
if atoms[i].symbol == A:
CN_AA_temp += 1
else: # atoms[i].symbol==B :
CN_AB_temp += 1
CN_AA += CN_AA_temp
CN_AB += CN_AB_temp
if len(indeces) < 12:
# SHELL
CNshellAA += CN_AA_temp
CNshellAB += CN_AB_temp
else:
# CORE
NAcore += 1
# averaging:
CN_AA = CN_AA * 1.0 / nA
CN_AB = CN_AB * 1.0 / nA
CN_BB = CN_BB * 1.0 / nB
CN_BA = CN_BA * 1.0 / nB
znam = (nA - NAcore)
if znam > 0.0001:
CNshellAA = CNshellAA * 1.0 / znam
CNshellAB = CNshellAB * 1.0 / znam
else:
CNshellAA = 0
CNshellAB = 0
znam = (nB - NBcore)
if znam > 0.0001:
CNshellBB = CNshellBB * 1.0 / znam
CNshellBA = CNshellBA * 1.0 / znam
else:
CNshellBB = 0
CNshellBA = 0
# calc concentrations:
concB = nB * 1.0 / N
if concB < 0.0001:
#print "WARNING! Too low B concentration: ",concB
etha = 999
else:
etha = 1 - CN_AB / (concB * (CN_AA + CN_AB))
R = atoms.positions.max() / 2.0
if calc_energy:
#from asap3 import EMT
from ase.calculators.emt import EMT
atoms.set_calculator(EMT())
E = atoms.get_potential_energy()
else:
E = -1
return N, nA, R, CN_AA, CN_AB, CN_BB, CN_BA, etha, E, NAcore, \
NBcore, CNshellAA, CNshellAB, CNshellBB, CNshellBA
def monoatomic(atoms, R1=3, calc_energy=False):
r"""This routine analyzes atomic structure
by the calculation of coordination numbers
in cluster with only one type of atom.
Parameters
----------
atoms: ase.Atoms
ase Atoms object, containing atomic cluster.
R1: float
First coordination shell will icnlude all atoms
with distance less then R1 [Angstrom].
Default value is 3.
calc_energy: bool
Flag used for calculation of potential energy with EMT
calculator. The default value is False, so that
energy is not calculated.
Returns
-------
N: int
number of atoms in cluster
R: float
radius of the cluster
CN: float
average coord number
E: float
potential energy, -1 if calc_energy is False
Ncore:
number of atoms in core region (number of atoms with
all 12 neighbors)
CNshell:
average coordination number for surface atoms only
Notes
-----
The radius of the cluster is roughly determined as
maximum the distance from the center to most distant atom
in the cluster.
Example
--------
>>> atoms = FaceCenteredCubic('Ag',
[(1, 0, 0), (1, 1, 0), (1, 1, 1)], [7,8,7], 4.09)
>>> [N, R, CN] = monoatomic(atoms)
>>> print "average CN is ", CN
"""
N = len(atoms)
nl = NeighborList([R1 / 2.0] * N, self_interaction=False, bothways=True)
nl.build(atoms)
CN = 0
Ncore = 0
Nshell = 0
CNshell = 0 # average CN of surface atoms
for i in xrange(0, N):
indeces, offsets = nl.get_neighbors(i)
CN += len(indeces)
if len(indeces) < 12:
Nshell += 1
CNshell += len(indeces)
else:
Ncore += 1
CN = CN * 1.0 / N
CNshell = CNshell * 1.0 / Nshell
atoms.center()
R = atoms.positions.max() / 2.0
if calc_energy:
#from asap3 import EMT
from ase.calculators.emt import EMT
atoms.set_calculator(EMT())
E = atoms.get_potential_energy()
else:
E = -1
return N, R, CN, E, Ncore, CNshell
