def analyse_angles(model, A, B, C):
'''
Check A-B distances present in the model.
model: Atoms object or string. If string it will read a file
in the same folder, e.g. "name.traj"
A: string, chemical symbol, e.g. "O"
B: string, chemical symbol, e.g. "C"
C: string, chemical symbol, e.g. "O"
'''
# Read file or Atoms object
if isinstance(model, str) is True:
model = read(model)
analysis = Analysis(model)
dash = "-"*40
print_ABC = A + "-" + B + "-" + C
# Retrieve bonds and values
ABC_Angle = analysis.get_angles(A, B, C)
ABC_AngleValues = analysis.get_values(ABC_Angle)
# Table header
print(dash)
print(print_ABC+" Angle / Degrees")
print(dash)
print('{:<6.5s}{:>4.10s}{:^13.10s}{:>4.10s}'.format(
"count", "average", "minimum", "maximum"))
# Table contents
print('{:<6.0f}{:>4.4f}{:^12.4f}{:>4.4f}'.format(
len(ABC_Angle[0]), np.average(ABC_AngleValues),
np.amin(ABC_AngleValues), np.amax(ABC_AngleValues)))
def test_analysis():
#test the geometry.analysis module
mol = molecule('CH3CH2OH')
ana = Analysis(mol)
assert np.shape(ana.adjacency_matrix[0].todense()) == (9, 9)
for imI in range(len(ana.all_bonds)):
l1 = sum([len(x) for x in ana.all_bonds[imI]])
l2 = sum([len(x) for x in ana.unique_bonds[imI]])
assert l1 == l2 * 2
for imi in range(len(ana.all_angles)):
l1 = sum([len(x) for x in ana.all_angles[imi]])
l2 = sum([len(x) for x in ana.unique_angles[imi]])
assert l1 == l2 * 2
for imi in range(len(ana.all_dihedrals)):
l1 = sum([len(x) for x in ana.all_dihedrals[imi]])
l2 = sum([len(x) for x in ana.unique_dihedrals[imi]])
assert l1 == l2 * 2
assert len(ana.get_angles('C', 'C', 'H', unique=False)[0]) == len(
ana.get_angles('C', 'C', 'H', unique=True)[0]) * 2
csixty = molecule('C60')
mol = molecule('C7NH5')
ana = Analysis(csixty)
ana2 = Analysis(mol)
for imI in range(len(ana.all_bonds)):
l1 = sum([len(x) for x in ana.all_bonds[imI]])
l2 = sum([len(x) for x in ana.unique_bonds[imI]])
assert l1 == l2 * 2
for imI in range(len(ana.all_angles)):
l1 = sum([len(x) for x in ana.all_angles[imI]])
l2 = sum([len(x) for x in ana.unique_angles[imI]])
assert l1 == l2 * 2
for imI in range(len(ana.all_dihedrals)):
l1 = sum([len(x) for x in ana.all_dihedrals[imI]])
l2 = sum([len(x) for x in ana.unique_dihedrals[imI]])
assert l1 == l2 * 2
assert len(ana2.get_angles('C', 'C', 'H', unique=False)[0]) == len(
ana2.get_angles('C', 'C', 'H', unique=True)[0]) * 2
assert len(ana2.get_dihedrals('H', 'C', 'C', 'H', unique=False)[0]) == len(
ana2.get_dihedrals('H', 'C', 'C', 'H', unique=True)[0]) * 2
def analyse_all_angles(model):
'''
Returns a table of bond angle analysis for the supplied model.
Parameters:
model: Atoms object or string. If string it will read a file
in the same folder, e.g. "name.traj"
'''
# Product to get all possible arrangements
from itertools import product
# Read file or Atoms object
if isinstance(model, str) is True:
model = read(model)
analysis = Analysis(model)
dash = "-" * 40
# set() to ensure unique chemical symbols list
list_of_symbols = list(set(model.get_chemical_symbols()))
all_angles = product(list_of_symbols, repeat=3)
# Table heading
print(dash)
print('{:<9.8s}{:<6.5s}{:>4.10s}{:^13.10s}{:>4.10s}'.format(
"Angle", "Count", "Average", "Minimum", "Maximum"))
print(dash)
# Iterate over all arrangements of chemical symbols
for angles in all_angles:
A = angles[0]
B = angles[1]
C = angles[2]
print_ABC = A + '-' + B + '-' + C
ABC_Angle = analysis.get_angles(A, B, C)
# Make sure angles exist before retrieving values, print table contents
if not ABC_Angle == [[]]:
ABC_AngleValues = analysis.get_values(ABC_Angle)
print('{:<9.8s}{:<6.0f}{:>4.4f}{:^12.4f}{:>4.4f}'.format(
print_ABC, len(ABC_Angle[0]), np.average(ABC_AngleValues),
np.amin(ABC_AngleValues), np.amax(ABC_AngleValues)))
def analyse_angles(model, A, B, C, verbose=True, multirow=False):
'''
Check A-B-C angles present in the model.
Parameters:
model: Atoms object
XXX
A: string, chemical symbol, e.g. "O"
B: string, chemical symbol, e.g. "C"
C: string, chemical symbol, e.g. "O"
verbose: Boolean
Whether to print information to screen
multirow: Boolean
Whether we are returning multiple sets of results in a Table
'''
from ase.geometry.analysis import Analysis
analysis = Analysis(model)
print_ABC = A + "-" + B + "-" + C
# Retrieve bonds and values
ABC_indices = analysis.get_angles(A, B, C)
if len(ABC_indices[0]) == 0:
ABC_values = None
else:
ABC_values = analysis.get_values(ABC_indices)
if verbose and ABC_values is not None:
# Table header
if not multirow:
print_angles_table_header()
# Table contents
import numpy as np
print('{:<9.8s}{:<6.0f}{:>4.4f}{:^12.4f}{:>4.4f}'.format(
print_ABC, len(ABC_indices[0]), np.average(ABC_values),
np.amin(ABC_values), np.amax(ABC_values)))
return ABC_indices, ABC_values
SnIBondValues = ana.get_values(SnIBonds)
#print("The average Pb-I bond length is {}.".format(np.average(PbIBondValues)))
#print("The average Sn-I bond length is {}.".format(np.average(SnIBondValues)))
if len(PbIBonds[0]) > 0:
AllPbIBonds.append(np.average(PbIBondValues))
if len(SnIBonds[0]) > 0:
AllSnIBonds.append(np.average(SnIBondValues))
#
# Angles
IPbIAngles = ana.get_angles('I', 'Pb', 'I', unique=True)
ISnIAngles = ana.get_angles('I', 'Sn', 'I', unique=True)
PbIPbAngles = ana.get_angles('Pb', 'I', 'Pb', unique=True)
SnISnAngles = ana.get_angles('Sn', 'I', 'Sn', unique=True)
#print("\nThere are {} I-Pb-I angles in PEA2PbSnI4.".format(len(IPbIAngles[0])))
#print("There are {} I-Sn-I angles in PEA2PbSnI4.".format(len(ISnIAngles[0])))
if len(IPbIAngles[0]) > 0:
IPbIAngleValues = ana.get_values(IPbIAngles)
IPbIAngleValuesOver120 = np.array(IPbIAngleValues)[(
np.array(IPbIAngleValues) >= 120)]
AllPbIAngles.append(np.average(IPbIAngleValuesOver120))
if len(PbIPbAngles[0]) > 0:
PbIPbAngleValues = ana.get_values(PbIPbAngles)
for imI in range(len(ana.all_bonds)):
l1 = sum([len(x) for x in ana.all_bonds[imI]])
l2 = sum([len(x) for x in ana.unique_bonds[imI]])
assert l1 == l2 * 2
for imi in range(len(ana.all_angles)):
l1 = sum([len(x) for x in ana.all_angles[imi]])
l2 = sum([len(x) for x in ana.unique_angles[imi]])
assert l1 == l2 * 2
for imi in range(len(ana.all_dihedrals)):
l1 = sum([len(x) for x in ana.all_dihedrals[imi]])
l2 = sum([len(x) for x in ana.unique_dihedrals[imi]])
assert l1 == l2 * 2
assert len(ana.get_angles('C','C','H', unique=False)[0]) == len(ana.get_angles('C','C','H', unique=True)[0])*2
csixty = molecule('C60')
mol = molecule('C7NH5')
ana = Analysis(csixty)
ana2 = Analysis(mol)
for imI in range(len(ana.all_bonds)):
l1 = sum([len(x) for x in ana.all_bonds[imI]])
l2 = sum([len(x) for x in ana.unique_bonds[imI]])
assert l1 == l2 * 2
for imI in range(len(ana.all_angles)):
l1 = sum([len(x) for x in ana.all_angles[imI]])
l2 = sum([len(x) for x in ana.unique_angles[imI]])
assert l1 == l2 * 2
from ase.io.trajectory import Trajectory
import numpy as np
from ase.io import read
from ase.geometry.analysis import Analysis
#old file see bonds.py for better version
file = read('tin_acetate.xyz')
traj = Trajectory('tin_acetate.traj', 'w')
traj.write(file)
file = read('tin_acetate.traj')
ana = Analysis(file)
SiOBonds = ana.get_bonds('Sn', 'O')
SiOSiAngles = ana.get_angles('O', 'Sn', 'O')
print("there are {} Si-O bonds in BETA".format(len(SiOBonds[0])))
print("there are {} Si-O-Si angles in BETA".format(len(SiOSiAngles[0])))
SiOBondsValues = ana.get_values(SiOBonds)
SiOSiAngleValues = ana.get_values(SiOSiAngles)
print("bond length data:")
print("the average Si-O bond length is {}.".format(np.average(SiOBondsValues)))
print("the minimum Si-O Distance is:", np.amin(SiOBondsValues))
print("the maximum Si-O Distance is:", np.amax(SiOBondsValues))
print("bond angle data:")
print("the average Si-O-Si angle is {}.".format(np.average(SiOSiAngleValues)))
print("the maximum Si-O-Si angle is:", np.amax(SiOSiAngleValues))
print("the minimum Si-O-Si angle is:", np.amin(SiOSiAngleValues))
from ase.io.trajectory import Trajectory
import numpy as np
from ase.io import read
from ase.geometry.analysis import Analysis
BEA = read('BEA.cif')
traj = Trajectory('BEA.traj', 'w')
traj.write(BEA)
BEA = read('BEA.traj')
ana = Analysis(BEA)
SiOBonds = ana.get_bonds('Si', 'O')
SiOSiAngles = ana.get_angles('Si', 'O', 'Si')
print("there are {} Si-O bonds in BETA".format(len(SiOBonds[0])))
print("there are {} Si-O-Si angles in BETA".format(len(SiOSiAngles[0])))
SiOBondsValues = ana.get_values(SiOBonds)
SiOSiAngleValues = ana.get_values(SiOSiAngles)
print("bond length data:")
print("the average Si-O bond length is {}.".format(np.average(SiOBondsValues)))
print("the minimum Si-O Distance is:", np.amin(SiOBondsValues))
print("the maximum Si-O Distance is:", np.amax(SiOBondsValues))
print("bond angle data:")
print("the average Si-O-Si angle is {}.".format(np.average(SiOSiAngleValues)))
print("the maximum Si-O-Si angle is:", np.amax(SiOSiAngleValues))
print("the minimum Si-O-Si angle is:", np.amin(SiOSiAngleValues))