from XRDTools.Diffractometer import Diffractometer
from XRDTools.Geometry import two_theta_2_wave_vector_length
from XRDTools.Spectrum import centroid, calculate_ag, estimate_noise_level
from XRDTools.Functions import ag_fct
from lmfit import Model
data_path = 'Data/'
sample_tuples = [
# ('T2T_22_24_STO.dat',(22,24)),
# ('T2T_22_23p5_LSAT.dat',(22,23.5)),
('thickness_PCCO.dat', (28, 30.5))
]
dm = Diffractometer()
wave_length = dm.wave_length
fig = plt.figure()
AX1 = fig.add_subplot(1, 2, 1)
AX2 = fig.add_subplot(2, 2, 2)
AX3 = fig.add_subplot(2, 2, 4)
AX1.set_yscale('log')
AX3.set_yscale('log')
# ag_fct(x,wave_vector_g,thickness,sigma_eps,scale,noise)
ag_model = Model(ag_fct)
params = ag_model.make_params()
params['wave_vector_g'].vary = False
params['thickness'].value = 60
from XRDTools.CristalStructure import Cubic
from XRDTools.Diffractometer import Diffractometer
import numpy as np
# Build unit cell. Using atomic number as atomic factor
STO = Cubic(0.3905)
STO.add_atom((0,0,0),38,label = 'Sr')
STO.add_atom((0.5,0.5,0.5),22,label = 'Ti')
STO.add_atom((0.5,0.5,0),8,label = 'O1')
STO.add_atom((0.5,0,0.5),8,label = 'O2')
STO.add_atom((0,0.5,0.5),8,label = 'O3')
# Orientation of normal and in plane of the cristal
hkl_z = (0,0,1)
pqr_x = (1,0,0)
# Put the sample in the diffractometer with the right orientation
dm = Diffractometer(cristal_structure = STO, surface_normal_hkl = hkl_z,azimuth_pqr = pqr_x)
# Show some peaks values
HKL = (0,0,2)
print('hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'.format(*HKL,dm.hkl_2_two_theta(HKL),*dm.hkl_2_theta_source_theta_detector_phi(HKL),STO.structure_factor(HKL)))
HKL = (1,0,3)
print('hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'.format(*HKL,dm.hkl_2_two_theta(HKL),*dm.hkl_2_theta_source_theta_detector_phi(HKL),STO.structure_factor(HKL)))
HKL = (0,1,3)
print('hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'.format(*HKL,dm.hkl_2_two_theta(HKL),*dm.hkl_2_theta_source_theta_detector_phi(HKL),STO.structure_factor(HKL)))
ETO_prim.add_atom((0.706533, 0.293467, 0.293467),8,'O')
ETO_prim.add_atom((0.956533, 0.543467, 0.543467),8,'O')
ETO_prim.add_atom((0.293467, 0.293467, 0.706533),8,'O')
ETO_prim.add_atom((0.706533, 0.293467, 0.706533),8,'O')
ETO_prim.add_atom((0.293467, 0.706533, 0.293467),8,'O')
ETO_prim.add_atom((0.706533, 0.706533, 0.293467),8,'O')
ETO_prim.add_atom((0.293467, 0.706533, 0.706533),8,'O')
ETO_prim.add_atom((0.956533, 0.543467, 0.956533),8,'O')
ETO_prim.add_atom((0.543467, 0.956533, 0.543467),8,'O')
ETO_prim.add_atom((0.543467, 0.956533, 0.956533),8,'O')
ETO_prim.add_atom((0.543467, 0.543467, 0.956533),8,'O')
ETO_prim.add_atom((0.956533, 0.956533, 0.543467),8,'O')
hkl_z = (1,1,1)
dm = Diffractometer(cristal_structure = ETO_prim, surface_normal_hkl = hkl_z)
# pqr_x = (1,0,0)
# # Show some peaks values
HKL = (2,2,2)
print('hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'.format(*HKL,dm.hkl_2_two_theta(HKL),*dm.hkl_2_theta_source_theta_detector(HKL),0,np.abs(ETO_prim.structure_factor(HKL))**2))
HKL = (6,4,4)
print('hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'.format(*HKL,dm.hkl_2_two_theta(HKL),*dm.hkl_2_theta_source_theta_detector(HKL),0,np.abs(ETO_prim.structure_factor(HKL))**2))
HKL = (4,4,2)
print('hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'.format(*HKL,dm.hkl_2_two_theta(HKL),*dm.hkl_2_theta_source_theta_detector(HKL),0,np.abs(ETO_prim.structure_factor(HKL))**2))
# Build unit cell. Using atomic number as atomic factor
from XRDTools.CristalStructure import Cubic, Rhombohedral
from XRDTools.Diffractometer import Diffractometer
from XRDTools.Geometry import two_theta_2_wave_vector_length
from XRDTools import wave_length
import numpy as np
# print(np.sqrt(3*(2**2))*2*np.pi/two_theta_2_wave_vector_length(wave_length,30.32))
YSZ = Cubic(0.5134)
hkl_z = (1, 1, 1)
dm = Diffractometer(cristal_structure=YSZ, surface_normal_hkl=hkl_z)
# pqr_x = (1,0,0)
# # Show some peaks values
HKL = (1, 1, 1)
print(
'hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'
.format(*HKL, dm.hkl_2_two_theta(HKL),
*dm.hkl_2_theta_source_theta_detector(HKL), 0,
np.abs(YSZ.structure_factor(HKL))**2))
HKL = (3, 1, 1)
print(
'hkl : {0:d}{1:d}{2:d}, 2T : {3:.4f}, Source : {4:.4f}, Detector : {5:.4f}, Phi : {6:.4f}, Factor : {7:.3f}'
.format(*HKL, dm.hkl_2_two_theta(HKL),
*dm.hkl_2_theta_source_theta_detector(HKL), 0,
np.abs(YSZ.structure_factor(HKL))**2))