from ioAndInterfaces import ccdcCrystalToASE
from ccdc.io import EntryReader
from ase.io import write as ASEWrite
csdEntryReader = EntryReader('CSD')
aseCrystal = ccdcCrystalToASE(csdEntryReader.crystal('ABEBUF'))
ASEWrite('temp.xyz', aseCrystal)
class CSD_powder:
"""
CSD_powder class
#######################
this class calculates d_spacing, intensities and two theta for a specific crystal
Attributes
-------------
entry [ccdc entry reader method]
crystal_name str the name of a crystal of form 'AABHTZ'
Methods
---------------
__init__()
---------------
takes 2 arguments self,name [str]
sets crystal name
load_d_space()
---------------
uses name atr
calls ccdc PowderPattern class
calculates d_spacing using braggs law
returns d_space[list of d_spacing], intensities[list of peak intensities]
load_intensities()
------------------
uses name atr
calls ccdc PowderPattern class
returns list[intensities]
load_two_theta()
-------------------
uses name atr
calls ccdc PowderPattern class
returns list[two theta angles]
"""
def __init__(self):
self.entry = EntryReader('CSD')
def get_crystal_name(self):
return self.crystal_name
def set_crystal_name(self, value):
self.crystal_name = value
def load_d_space(self):
# creates a d_space list with intensities as a second option
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
self.wavelength = PowderPattern.Wavelength.Wavelength_CuKa1
peak_thetas = []
#intents = pattern.intensity
two_t = pattern.two_theta
intents = pattern.intensity # all pattern intensity
intensity = [] # final list of intensities
for i in pattern.tick_marks:
l = i.two_theta # two theta vals
for j, I in zip(two_t, intents):
if abs(l - j) < 0.01:
# compare lists and find peak 2theta values the above assumption may be changed
peak_thetas.append(j) # tick two theta val
intensity.append(
I) # add the intensity of those peaks to a list
break
d_space = [] # list of d_spaces
peak_thetas = np.array(peak_thetas) / 2 # theta vals instead of 2theta
peak_radians = peak_thetas * np.pi / 180 # to radians
for peak in peak_radians:
d = self.wavelength / (2 * np.sin(peak)
) # get the space values in Angstorms
d_space.append(d) # append final values to a list
return d_space, intensity
def load_intensities(self):
# loads the intensities of a given crsytal
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.intensity
def load_two_theta(self):
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.two_theta
def get_data(self, option):
if option == 1:
d_space, intensities = self.load_d_space()
for i, j in zip(d_space, intensities):
print i, j
if option == 2:
"""all the data"""
x1 = self.load_intensities()
x2 = self.load_two_theta()
for i, j in zip(x1, x2):
print i, j
else:
sys.exit(1)
class CSD_powder:
"""
CSD_powder class
#######################
this class calculates d_spacing, intensities and two theta for a specific crystal
Attributes
-------------
entry [ccdc entry reader method]
crystal_name str the name of a crystal of form 'AABHTZ'
Methods
---------------
__init__()
---------------
takes 2 arguments self,name [str]
sets crystal name
load_d_space()
---------------
uses name atr
calls ccdc PowderPattern class
calculates d_spacing using braggs law
returns d_space[list of d_spacing], intensities[list of peak intensities]
load_intensities()
------------------
uses name atr
calls ccdc PowderPattern class
returns list[intensities]
load_two_theta()
-------------------
uses name atr
calls ccdc PowderPattern class
returns list[two theta angles]
"""
def __init__(self):
self.entry = EntryReader('CSD')
def get_crystal_name(self):
return self.crystal_name
def set_crystal_name(self,value):
self.crystal_name = value
def load_d_space(self):
# creates a d_space list with intensities as a second option
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
self.wavelength = PowderPattern.Wavelength.Wavelength_CuKa1
peak_thetas = []
#intents = pattern.intensity
two_t = pattern.two_theta
intents = pattern.intensity # all pattern intensity
intensity = [] # final list of intensities
for i in pattern.tick_marks:
l = i.two_theta # two theta vals
for j,I in zip(two_t,intents):
if abs(l-j) < 0.01:
# compare lists and find peak 2theta values the above assumption may be changed
peak_thetas.append(j) # tick two theta val
intensity.append(I) # add the intensity of those peaks to a list
break
d_space = [] # list of d_spaces
peak_thetas = np.array(peak_thetas)/2 # theta vals instead of 2theta
peak_radians = peak_thetas*np.pi/180 # to radians
for peak in peak_radians:
d = self.wavelength/(2*np.sin(peak)) # get the space values in Angstorms
d_space.append(d) # append final values to a list
return d_space,intensity
def load_intensities(self):
# loads the intensities of a given crsytal
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.intensity
def load_two_theta(self):
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.two_theta
def get_data(self,option):
if option == 1:
d_space,intensities = self.load_d_space()
for i,j in zip(d_space,intensities):
print i,j
if option == 2:
"""all the data"""
x1 = self.load_intensities()
x2 = self.load_two_theta()
for i,j in zip(x1,x2):
print i,j
else:
sys.exit(1)
