u.verbosity = args.verbosity
nsteps = args.nsteps
if nsteps:
step = (args.max - args.min) / nsteps
SpecRange = np.arange(args.min, args.max + 1, step)
else:
step = args.step
SpecRange = np.arange(args.min, args.max + 1, step)
nsteps = len(SpecRange)
if u.verbosity >= 1:
print
print(u.banner(ch='#', length=80))
print(title)
print(u.banner(ch='#', length=80))
print
#
# Recapitulation of input files
#
if u.verbosity >= 1:
print(" > READING INPUT FILES...")
print
# if u.verbosity >= 2:
print(" Dipole orientation file : %s" % infile)
print(" Structure file : %s" % structure)
print
def make_dipo(dipole, dipole_types, coords):
dip_type = dipole[0]
dip_s = np.sqrt(dipole_types[dip_type][0])
dip_ori = dipole[1:]
# Orient dipole along an interatomic axis
if len(dip_ori) == 2:
# -1 to adapt to Python numeration
a = coords[dip_ori[0] - 1]
b = coords[dip_ori[1] - 1]
direction = (b - a) / np.linalg.norm(b - a)
# dip = dip_s * direction
dip = direction
if u.verbosity >= 2:
print(" Dipole oriented along %s." % ', '.join(u.compact_extended_list(dip_ori)))
# Orient dipole along an interatomic axis and forming and angle
# theta with the plane defined by 3 atoms
elif len(dip_ori) == 4:
# -1 to adapt to Python numeration
a = coords[dip_ori[0] - 1]
b = coords[dip_ori[1] - 1]
c = coords[dip_ori[2] - 1]
theta = dip_ori[3]
# Generate a reference frame from point a, b, c
# Our desired direction is b - a, i.e. the x axis
# of this new ref frame. (see refframe function in
# util.py
ref = u.refframe(a, b, c)
cartesian = np.eye(3)
# Define transformation matrices
T = np.dot(cartesian, ref.T)
Ry = u.rot_mat_y(theta)
# Ry is 4x4, reduce it to 3x3
Ry = Ry[:3,:3]
x = cartesian[0]
direction = np.dot(x, Ry)
direction = np.dot(direction, T.T)
# dip = dip_s * direction
dip = direction
if u.verbosity >= 2:
print(" Dipole oriented out of the plane defined by %s by %5.2f degrees." % \
(', '.join(u.compact_extended_list(dip_ori[:-1])), theta))
else:
print(u.banner(text='ERROR', ch='#', length=80))
print("Unrecognized number of parameters for dipole orientation.")
print
sys.exit()
return dip
def parse_input(infile):
'''Returns a Dictionary with dipole types,
and a list of tuples for points of application of the dipoles.
The keys of dipole types dictionary are the flags set ny the user in the input.
Each value is a tuple. The first element of the tuple is a list containing the
Dipolar Strength, the Excitation energy and the damping. The second element of
the tuple is a flag defining the type of polarizability to calculate (electric or
magnetic). The third element of the tuple if present only for magnetic polarizabilities
and it is the bj coefficient.
For application points, the data are tuples of 3 elements.
Each tuple contains, as first element, the center expressed in terms
of atom indexes and, as second element, the weight to be applied on the
first element of the list. As third element, we have a list of dipoles to be applied
in that point. The dipole is described through a list containing the dipole
type and its orientation, in terms of atomic indexes.'''
u.checkfile(infile)
type_counter = 0
center_counter = 0
dipole_types = {}
centers = []
with open(infile) as f:
while True:
line = f.readline()
if not line:
break
if line.strip():
if line.startswith('#'):
continue
# Create Dipole Types Dictionary
elif line.split()[0].lower() == 'type':
type_counter += 1
type_flag = line.split()[1]
# Try to read TYPE definition without optional keyword
try:
dipole = map(float, line.split()[2:])
pol_type = 'ele'
dipole_types[type_flag] = (map(float, line.split()[2:]), pol_type)
# Read TYPE definition with optional keyword
except ValueError:
pol_type = line.split()[-2]
bj = float(line.split()[-1])
dipole_types[type_flag] = (map(float, line.split()[2:-2]), pol_type, bj)
type_counter += 1
# Centers
elif line.split()[0].lower() == 'center':
center_counter += 1
weight = float(line.split()[1])
atom_idx = u.extend_compact_list(line.split()[2:])
# Adjust indices to Python's numeration
atom_idx = map(lambda x: x - 1, atom_idx)
data = f.readline().strip()
# Retrieve dipoles applied in this center
dipoles = []
while True:
if not data or data.split()[0].lower() != 'dipole':
break
data = data.split()
dip_type = [data[1]]
dip_ori = data[2:]
if len(dip_ori) == 2:
dip_ori = u.extend_compact_list(dip_ori)
elif len(dip_ori) > 2:
theta = float(dip_ori[-1])
dip_ori = u.extend_compact_list(dip_ori[:-1])
dip_ori = dip_ori + [theta]
dipole = dip_type + dip_ori
dipoles.append(dipole)
data = f.readline().strip()
centers.append((atom_idx, weight, dipoles))
# Dipoles
elif line.split()[0].lower() == 'dipole':
if center_counter == 0:
print(u.banner(text='ERROR', ch='#', length=80))
print
print(" You defined a DIPOLE before assigning it a CENTER in %s" % infile)
print
sys.exit()
# dipole_counter += 1
if type_counter == 0:
print(u.banner(text='ERROR', ch='#', length=80))
print
print(" No dipole TYPE has been defined in %s" % infile)
print
sys.exit()
return dipole_types, centers
