def main():
structure = XYZ()
structure.load(structure_file)
atom_numbers = get_atom_numbers_by_z_range(structure.rows, surface_z_min,
surface_z_max)
f = file(output_file, 'w')
for atom_number in atom_numbers:
f.write(str(atom_number) + "\n")
f.close()
def main():
structure = XYZ()
structure.load(structure_file)
atom_numbers = get_atom_numbers_by_z_range(
structure.rows, surface_z_min, surface_z_max
)
f = file(output_file, 'w')
for atom_number in atom_numbers:
f.write(str(atom_number)+"\n")
f.close()
def main():
structure = XYZ()
structure.load(structure_file)
structure.set_rows(
get_atoms_by_z_range(structure.rows, surface_z_min, surface_z_max))
structure.export(output_file)
def main():
structure = XYZ()
structure.load(structure_file)
structure.set_rows(
get_atoms_by_z_range(structure.rows, surface_z_min, surface_z_max)
)
structure.export(output_file)
def initialize(self):
self.number_of_target_atoms = Struct()
self.number_of_target_atoms.x = len(self.molecule_placement[0])
self.number_of_target_atoms.y = len(self.molecule_placement)
self.spacing_of_target_atoms = Struct()
self.spacing_of_target_atoms.x = abs(self.upper_left_surface_atom.x- \
self.lower_right_surface_atom.x)/(self.number_of_target_atoms.x-1) #-1 because counting atom connections
self.spacing_of_target_atoms.y = abs(self.upper_left_surface_atom.y- \
self.lower_right_surface_atom.y)/(self.number_of_target_atoms.y-1) #-1 because counting atom connections
#Load our surface and molecule placing position
self.surface = XYZ()
self.surface.load(self.surface_xyz_file)
self.place_molecule = XYZ()
self.place_molecule.load(self.place_xyz_file)
self.place_molecule.normalize_coordinates(
) #Make the molecule start from (0,0,0)
#Make the molecule start from the upper left position
self.place_molecule.translate(self.upper_left_surface_atom.x, self.upper_left_surface_atom.y, \
self.upper_left_surface_atom.z)
def initialize(self):
self.number_of_target_atoms = Struct()
self.number_of_target_atoms.x = len(self.molecule_placement[0])
self.number_of_target_atoms.y = len(self.molecule_placement)
self.spacing_of_target_atoms = Struct()
self.spacing_of_target_atoms.x = abs(self.upper_left_surface_atom.x - self.lower_right_surface_atom.x) / (
self.number_of_target_atoms.x - 1
) # -1 because counting atom connections
self.spacing_of_target_atoms.y = abs(self.upper_left_surface_atom.y - self.lower_right_surface_atom.y) / (
self.number_of_target_atoms.y - 1
) # -1 because counting atom connections
# Load our surface and molecule placing position
self.surface = XYZ()
self.surface.load(self.surface_xyz_file)
self.place_molecule = XYZ()
self.place_molecule.load(self.place_xyz_file)
self.place_molecule.normalize_coordinates() # Make the molecule start from (0,0,0)
# Make the molecule start from the upper left position
self.place_molecule.translate(
self.upper_left_surface_atom.x, self.upper_left_surface_atom.y, self.upper_left_surface_atom.z
)
import XYZ
from datetime import date
inputs = {'uid' : 12345,
'issue' : date(2016, 1, 1),
'maturity' : date(2026, 1, 1),
'CouponFreq' : 2,
'coupon' : 0.05,
'price' : 115,
'PricingDate' : date(2016, 11, 17)
}
b = XYZ.Bond(inputs)
b.Print()
print('-----------------------------------')
b.verbose = True
p = b.YieldToPrice(0.05)
b.verbose = False
clean = b.YieldToPrice(0.05, clean=True)
print('Dirty Price : ', "{:10.4f}%".format(p*100))
print('Clean Price : ', "{:10.4f}%".format(clean*100))
print(' Accrued : ', "{:10.4f}%".format(b.data['accrued']*100))
print('-----------------------------------')
y = b.PriceToYield(p)
print('Yield : ', "{:10.4f}%".format(y*100))
b.data['yield'] = y
delta = b.Duration()
print('Delta : ', "{:10.4f}".format(delta))
class Surface_place:
def __init__(self):
pass
def set_filenames(self, in_surface_file, in_place_file, in_output_file):
self.surface_xyz_file = in_surface_file
self.place_xyz_file = in_place_file # The molecule we want to place on the surface
self.output_xyz_file = in_output_file
def define_surface_sites(self, in_upper_left, in_lower_right, in_z_dist):
self.upper_left_surface_atom = in_upper_left # In Angstroms
self.lower_right_surface_atom = in_lower_right
self.placement_z_distance_from_surface = in_z_dist
def define_molecule_placement(self, in_placement_config):
self.molecule_placement = in_placement_config
def initialize(self):
self.number_of_target_atoms = Struct()
self.number_of_target_atoms.x = len(self.molecule_placement[0])
self.number_of_target_atoms.y = len(self.molecule_placement)
self.spacing_of_target_atoms = Struct()
self.spacing_of_target_atoms.x = abs(self.upper_left_surface_atom.x - self.lower_right_surface_atom.x) / (
self.number_of_target_atoms.x - 1
) # -1 because counting atom connections
self.spacing_of_target_atoms.y = abs(self.upper_left_surface_atom.y - self.lower_right_surface_atom.y) / (
self.number_of_target_atoms.y - 1
) # -1 because counting atom connections
# Load our surface and molecule placing position
self.surface = XYZ()
self.surface.load(self.surface_xyz_file)
self.place_molecule = XYZ()
self.place_molecule.load(self.place_xyz_file)
self.place_molecule.normalize_coordinates() # Make the molecule start from (0,0,0)
# Make the molecule start from the upper left position
self.place_molecule.translate(
self.upper_left_surface_atom.x, self.upper_left_surface_atom.y, self.upper_left_surface_atom.z
)
def place(self):
for row_index, row in enumerate(self.molecule_placement):
for spot_index, each_spot in enumerate(row):
# We check for any list type first so that we can make modifications
# before doing translation and placing.
if each_spot != 0:
temp_place_molecule = copy.deepcopy(self.place_molecule)
if [].__class__ == type(each_spot): # If it is a list
print "Rotating molecule: " + str(each_spot[1])
# Rotate the molecule
temp_place_molecule.rotate_wrt_atom(each_spot[1], each_spot[2], each_spot[3])
each_spot = each_spot[0] # Set equal to just an integer so we can translate it later
# if type(1) == type(each_spot): #If integer
if each_spot == 1:
print "Placing molecule at: (" + str(spot_index) + ", " + str(row_index) + ")"
# We have a spot marked for placement. Let's place the molecule
# Note: We *must* use deepcopy since the XYZ class uses lists which
# are references.
temp_place_molecule.translate( # In initialize, we already translated to upper left position.
spot_index * self.spacing_of_target_atoms.x,
row_index * self.spacing_of_target_atoms.y,
self.placement_z_distance_from_surface,
)
# print spot_index * self.spacing_of_target_atoms.x
# print row_index * self.spacing_of_target_atoms.y
# print self.placement_z_distance_from_surface
self.surface.add(temp_place_molecule)
del temp_place_molecule # Don't need it since we added to the surface
class Surface_place:
def __init__(self):
pass
def set_filenames(self, in_surface_file, in_place_file, in_output_file):
self.surface_xyz_file = in_surface_file
self.place_xyz_file = in_place_file #The molecule we want to place on the surface
self.output_xyz_file = in_output_file
def define_surface_sites(self, in_upper_left, in_lower_right, in_z_dist):
self.upper_left_surface_atom = in_upper_left #In Angstroms
self.lower_right_surface_atom = in_lower_right
self.placement_z_distance_from_surface = in_z_dist
def define_molecule_placement(self, in_placement_config):
self.molecule_placement = in_placement_config
def initialize(self):
self.number_of_target_atoms = Struct()
self.number_of_target_atoms.x = len(self.molecule_placement[0])
self.number_of_target_atoms.y = len(self.molecule_placement)
self.spacing_of_target_atoms = Struct()
self.spacing_of_target_atoms.x = abs(self.upper_left_surface_atom.x- \
self.lower_right_surface_atom.x)/(self.number_of_target_atoms.x-1) #-1 because counting atom connections
self.spacing_of_target_atoms.y = abs(self.upper_left_surface_atom.y- \
self.lower_right_surface_atom.y)/(self.number_of_target_atoms.y-1) #-1 because counting atom connections
#Load our surface and molecule placing position
self.surface = XYZ()
self.surface.load(self.surface_xyz_file)
self.place_molecule = XYZ()
self.place_molecule.load(self.place_xyz_file)
self.place_molecule.normalize_coordinates(
) #Make the molecule start from (0,0,0)
#Make the molecule start from the upper left position
self.place_molecule.translate(self.upper_left_surface_atom.x, self.upper_left_surface_atom.y, \
self.upper_left_surface_atom.z)
def place(self):
for row_index, row in enumerate(self.molecule_placement):
for spot_index, each_spot in enumerate(row):
#We check for any list type first so that we can make modifications
#before doing translation and placing.
if each_spot != 0:
temp_place_molecule = copy.deepcopy(self.place_molecule)
if [].__class__ == type(each_spot): #If it is a list
print 'Rotating molecule: ' + str(each_spot[1])
#Rotate the molecule
temp_place_molecule.rotate_wrt_atom(
each_spot[1], each_spot[2], each_spot[3])
each_spot = each_spot[
0] #Set equal to just an integer so we can translate it later
#if type(1) == type(each_spot): #If integer
if each_spot == 1:
print 'Placing molecule at: (' + str(
spot_index) + ', ' + str(row_index) + ')'
#We have a spot marked for placement. Let's place the molecule
#Note: We *must* use deepcopy since the XYZ class uses lists which
# are references.
temp_place_molecule.translate( #In initialize, we already translated to upper left position.
spot_index * self.spacing_of_target_atoms.x,
row_index * self.spacing_of_target_atoms.y,
self.placement_z_distance_from_surface)
#print spot_index * self.spacing_of_target_atoms.x
#print row_index * self.spacing_of_target_atoms.y
#print self.placement_z_distance_from_surface
self.surface.add(temp_place_molecule)
del temp_place_molecule #Don't need it since we added to the surface
