def get_cs():
import pyasf
sp = pyasf.sp
np = pyasf.np
delta_1 = sp.Symbol("delta_Ti", real=True)
delta_2 = sp.Symbol("delta_O1", real=True)
delta_3 = sp.Symbol("delta_O2", real=True)
cs = pyasf.unit_cell(SpaceGroup)
cs.add_atom("Sr1", (0,0,0), 1, dE=-2)
cs.add_atom("Ti1", (sp.S("1/2"),sp.S("1/2"),sp.S("1/2") - delta_1), 1, dE=14.5)
cs.add_atom("O1", (sp.S("1/2"),sp.S("1/2"),0 + delta_2), 1)
cs.add_atom("O2", (sp.S("1/2"),0,sp.S("1/2") + delta_3), 1)
cs.subs[cs.a] = 3.9998
cs.subs[cs.c] = 4.0180
cs.subs[delta_1] = 0.018
cs.subs[delta_2] = 0.016
cs.subs[delta_3] = 0.015
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
def get_cs():
import pyasf
sp = pyasf.sp
cs = pyasf.unit_cell(SpaceGroup)
delta = sp.Symbol("delta", real=True, nonnegative=True)
x = sp.Symbol("x", real=True, nonnegative=True)
cs.add_atom("Y", (sp.S(0.1344), sp.S(0.1687), 0), 1)
cs.add_atom("FeP", (sp.S(0.3898), sp.S(0.3534), sp.S("1/2")), 0, occupancy = x*delta) # 4h pyramidal position
cs.add_atom("MnP", (sp.S(0.3898), sp.S(0.3534), sp.S("1/2")), 0, occupancy = 1 - x*delta) # 4h pyramidal position
cs.add_atom("FeO", (0, sp.S("1/2"), sp.S(0.251)), 0, occupancy = x * (1 - delta)) # 4f octahedral position
cs.add_atom("MnO", (0, sp.S("1/2"), sp.S(0.251)), 0, occupancy = 1 - x * (1 - delta)) # 4f octahedral position
cs.add_atom("O1", (0, 0, sp.S(0.260)), 1)
cs.add_atom("O2", (sp.S(0.1601), sp.S(0.4417), 0), 1)
cs.add_atom("O3", (sp.S(0.1523), sp.S(0.4291), sp.S("1/2")), 1)
cs.add_atom("O4", (sp.S(0.3930), sp.S(0.2028), sp.S(0.2415)), 1)
cs.get_tensor_symmetry()
cs.build_unit_cell()
cs.subs[cs.a]=7.3121
cs.subs[cs.b]=8.5397
cs.subs[cs.c]=5.7115
return cs
def get_cs():
import pyasf
sp = pyasf.sp
np = pyasf.np
delta_1 = 0
delta_2 = 0
delta_3 = 0
cs = pyasf.unit_cell(SpaceGroup)
cs.add_atom("Sr", (0,0,0), 1, dE=-4)
cs.add_atom("Ti", (sp.S("1/2"),sp.S("1/2"),sp.S("1/2") - delta_1), 1, dE=14.5)
cs.add_atom("O1", (sp.S("1/2"),sp.S("1/2"),0 + delta_2), 1)
cs.add_atom("O2", (sp.S("1/2"),0,sp.S("1/2") + delta_3), 1)
cs.subs[cs.a] = 3.905 - 1.3e-4
cs.subs[cs.c] = 3.905 + 5e-3
cs.subs[delta_1] = 0.0
cs.subs[delta_2] = 0.0
cs.subs[delta_3] = 0.0
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
def get_cs():
import pyasf
sp = pyasf.sp
cs = pyasf.unit_cell(ciffile)
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
def get_cs(T = 298., LT = False):
import pyasf
sp = pyasf.sp
if LT:
ciffile = "cif/RDP_orthorhombic_146K.cif"
ciffile = os.path.join(os.path.split(__file__)[0], ciffile)
cs = pyasf.unit_cell(ciffile, resonant="Rb")
else:
ciffile = "cif/RDP_tetragonal_RT.cif"
ciffile = os.path.join(os.path.split(__file__)[0], ciffile)
cs = pyasf.unit_cell(ciffile, resonant="Rb")
alpha_x = 0.0002262773722627715 # expansion coefficient
alpha_z = 0.0004233576642335819 # expansion coefficient
cs.subs[cs.a] += alpha_x * (T - 298.)
cs.subs[cs.c] += alpha_z * (T - 298.)
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
def get_cs():
import pyasf
sp = pyasf.sp
x = sp.Symbol("x", real=True, unbounded=False)
cs = pyasf.unit_cell(SpaceGroup)
cs.add_atom("Ti", (0,0,0), 0)
cs.add_atom("O", (x, x, 0), 1)
cs.subs[cs.a]=4.5924
cs.subs[cs.c]=2.9575
cs.subs[x]=0.30499
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
def get_cs():
import pyasf
sp = pyasf.sp
cs = pyasf.unit_cell(SpaceGroup)
cs.add_atom("Ti", (0,0.3048,sp.S("1/2")), 0)
cs.add_atom("O1", (0,0.2208,0), 1)
cs.add_atom("O2", (0,0.3619,0), 1)
cs.add_atom("N", (0,0, 0.230), 1)
cs.get_tensor_symmetry()
cs.build_unit_cell()
cs.subs[cs.a]=3.7926
cs.subs[cs.b]=18.458
cs.subs[cs.c]=2.9774
return cs
def get_cs(**kwargs):
sp = pyasf.sp
np = pyasf.np
cs = pyasf.unit_cell(SpaceGroup)
cs.add_atom("Li", (0, 0, 0.2821), 1, assume_complex=True)
cs.add_atom("Ta", (0, 0, 0), 0, assume_complex=True)
cs.add_atom("O", (0.0534, 0.3396, 0.0695), 1, assume_complex=True)
cs.subs[cs.a] = 5.15428
cs.subs[cs.c] = 13.7835
if "temperature" in kwargs:
fac = TExp(kwargs["temperature"])
cs.subs[cs.a] *= fac[0,0]
cs.subs[cs.c] *= fac[2,2]
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
def get_cs(**kwargs):
import pyasf
sp = pyasf.sp
cs = pyasf.unit_cell(SpaceGroup)
cs.add_atom("Li", (0, 0, 0.2829), 1)
cs.add_atom("Nb", (0, 0, 0), 0)
cs.add_atom("O", (0.0492, 0.3446, 0.0647), 1)
cs.subs[cs.a] = 5.14829
cs.subs[cs.c] = 13.8631
if "temperature" in kwargs:
fac = TExp(kwargs["temperature"])
cs.subs[cs.a] *= fac[0,0]
cs.subs[cs.c] *= fac[2,2]
cs.get_tensor_symmetry()
cs.build_unit_cell()
return cs
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test13.dat")
data[:, 0] = pl.radians(data[:, 0])
#pl.ion()
R = 0, 0, 2
thickness = 1000
Energy = 10000
#struct = pyasf.unit_cell("1011117")
struct1 = pyasf.unit_cell("1011117") #MgO
struct2 = pyasf.unit_cell("1011117")
struct2.subs[struct2.a] *= 1.01 #strained layer
Sub = reflectivity.Substrate(struct1)
v_par = sp.Matrix([3, -2, -1])
v_perp = sp.Matrix([1, 1, 1])
Sub.calc_orientation(v_par, v_perp)
#Sub.set_Miller(R)
layer1 = reflectivity.Epitaxial_Layer(struct2, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal = reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
#crystal.calc_layer_Miller()
crystal.calc_g0_gH(Energy)
thBragg = float(Sub.calc_Bragg_angle(Energy).subs(Sub.structure.subs).evalf())
angle = pl.linspace(0.99, 1.01, 501) * thBragg
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test4.dat")
data[:,0] = pl.radians(data[:,0])
#pl.ion()
R = 0,0,4
thickness=1000
Energy=10000
#struct = pyasf.unit_cell("1011169")
struct = pyasf.unit_cell("1011117") #MgO
Sub=reflectivity.Substrate(struct)
v_par=sp.Matrix([1,-1,0])
v_perp=sp.Matrix([1,1,1])
Sub.calc_orientation(v_par, v_perp)
layer1=reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal=reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg= float(layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle=pl.linspace(0.997, 1.003,501)*thBragg
crystal.calc_reflectivity(angle, Energy)
layer1.calc_amplitudes(angle, Energy)
Sub.calc_amplitudes(angle, Energy)
def my_strain_profile(strainmax, straindepth, xmax=25, npoints=501):
x=np.linspace(0, xmax, 801)
strain=(strainmax*np.exp(-x)*(1+x))[::-1]
strain=np.delete(strain, 0)
return x*straindepth, strain
#pl.plot(tvector[1:], strain[::-1])
#pl.show()
Energy=8000
structsub = pyasf.unit_cell("1512124") #BaTiO3
structsub.get_tensor_symmetry()
structsub.build_unit_cell()
structsub.subs[structsub.a] = 3.9064
Sub=reflectivity.Substrate(structsub)
struct1=pyasf.unit_cell("1525437")
struct1.add_atom("Sr", [0,0,0])
struct1.AU_positions.pop("Ba1")
struct1.AU_formfactors.pop("Ba1")
struct1.U.pop("Ba1")
struct1.get_tensor_symmetry()
struct1.build_unit_cell()
import os
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test8.dat")
data[:,0] = pl.radians(data[:,0])
#pl.ion()
R = 0,0,1
thickness=1000
Energy=10000
struct = pyasf.unit_cell("1507756") #Ba O3 Ti
Sub=reflectivity.Substrate(struct)
v_par=sp.Matrix([1,0,0])
v_perp=sp.Matrix([0,0,1])
Sub.calc_orientation(v_par, v_perp)
layer1=reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal=reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg= float(layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle=pl.linspace(0.98, 1.02,501)*thBragg
crystal.calc_reflectivity(angle, Energy)
layer1.calc_amplitudes(angle, Energy)
Sub.calc_amplitudes(angle, Energy)
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import pylab
import pyasf
import sympy as sp
# <codecell>
cs = pyasf.unit_cell("LiNbO3_R3cH_Abrahams86_ICSD_61118.cif", resonant="Nb")
# <codecell>
cs.AU_positions # positions in asymmetric unit
# <codecell>
cs.AU_formfactorsDDc["Nb1"] # cartesian representation of dipole dipole form factor tensor in asymmetric unit
# <codecell>
cs.get_tensor_symmetry() # apply all symmetry constraints of space group to all tensors (debye waller U_ij, f_ij)
# <codecell>
cs.AU_formfactorsDDc["Nb1"] # now with symmetry
# <codecell>
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test7.dat")
#data[:,0] = pl.radians(data[:,0])
#pl.ion()
R = 0,0,2
thickness=1000
Energy=10000
#struct = pyasf.unit_cell("1011117")
struct = pyasf.unit_cell("cif/MgO_52026.cif") #MgO
Sub=reflectivity.Substrate(struct)
v_par=sp.Matrix([3,-2,-1])
v_perp=sp.Matrix([1,1,1])
Sub.calc_orientation(v_par, v_perp)
layer1=reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal=reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg= float(layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle=pl.linspace(0.988, 1.012,501)*thBragg
crystal.calc_reflectivity(angle, Energy)
layer1.calc_amplitudes(angle, Energy)
Sub.calc_amplitudes(angle, Energy)
strain=(strainmax*np.exp(-x)*(1+x))[::-1]
strain=np.delete(strain, 0)
return x*straindepth, strain
#pl.plot(tvector[1:], strain[::-1])
#pl.show()
fields=data.fields[1::40]
Energy=np.array([float(en) for en in fields])
Q=data["Q"]
structsub = pyasf.unit_cell("1512124") #BaTiO3
structsub.get_tensor_symmetry()
structsub.build_unit_cell()
structsub.feed_feff("ti", *feff.T)
structsub.subs[structsub.a] = 3.9064
Sub=reflectivity.Substrate(structsub)
struct1=pyasf.unit_cell("1525437")
struct1.add_atom("Sr", [0,0,0])
struct1.AU_positions.pop("Ba1")
struct1.AU_formfactors.pop("Ba1")
struct1.U.pop("Ba1")
struct1.get_tensor_symmetry()
struct1.build_unit_cell()
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test9.dat")
#data[:,0] = pl.radians(data[:,0])
#pl.ion()
R = 3, 0, 0
thickness = 1000
Energy = 10000
#struct = pyasf.unit_cell("1521772")
struct = pyasf.unit_cell("cif/LiNbO3_28294.cif") #Li Nb O3
Sub = reflectivity.Substrate(struct)
v_par = sp.Matrix([0, 0, 1])
v_perp = sp.Matrix([1, 0, 0]) #2,1,0
Sub.calc_orientation(v_par, v_perp)
layer1 = reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal = reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg = float(
layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle = pl.linspace(0.9955, 1.0045, 501) * thBragg
crystal.calc_reflectivity(angle, Energy)
layer1.calc_amplitudes(angle, Energy)
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test11.dat")
#data[:,0] = pl.radians(data[:,0])
#pl.ion()
R = 3,0,0
thickness=1000
Energy=10000
#struct = pyasf.unit_cell("1521772")
struct = pyasf.unit_cell("cif/LiNbO3_28294.cif") #Li Nb O3
Sub=reflectivity.Substrate(struct)
v_par=sp.Matrix([-1,1,4])#1,0,2
v_perp=sp.Matrix([1,1,0]) #1,2,0
Sub.calc_orientation(v_par, v_perp)
layer1=reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal=reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg= float(layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle=pl.linspace(0.992, 1.008,501)*thBragg
crystal.calc_reflectivity(angle, Energy)
R = 0,0,2
xmax=25
strainmax=0.0106
t=.62*1e4
x=np.linspace(0, xmax, 101)
strain=(strainmax*np.exp(-x)*(1+x))[::-1]
strain=np.delete(strain, 0)
tvector=(x*t)
#pl.plot(tvector[1:], strain[::-1])
#pl.show()
Energy=8000
structsub = pyasf.unit_cell("1507756") #BaTiO3
structsub.subs[structsub.a] = 3.9064
structsub.subs[structsub.c] = 3.9064
Sub=reflectivity.Substrate(structsub)
struct1=pyasf.unit_cell("1507756")
struct1.subs[struct1.a] = 3.9064
struct1.subs[struct1.c] = 3.9064
layer1=reflectivity.Strained_Layer(struct1, tvector, c=strain)
psi=0
v_perp=sp.Matrix([0,0,1])
Sub.calc_orientation_from_angle(psi, v_perp)
layer1.calc_orientation_from_angle(psi, v_perp)
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test12.dat")
#data[:,0] = pl.radians(data[:,0])
#pl.ion()
R = 0,0,2
thickness=1000
Energy=10000
#struct = pyasf.unit_cell("1011169")
struct1 = pyasf.unit_cell("1011117") #MgO
struct2 = pyasf.unit_cell("1011117")
struct2.subs[struct2.a] *= 1.01 #strained layer
Sub=reflectivity.Substrate(struct1)
v_par=sp.Matrix([1,0,0])
v_perp=sp.Matrix([0,0,1])
Sub.calc_orientation(v_par, v_perp)
layer1=reflectivity.Epitaxial_Layer(struct2, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal=reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg= float(Sub.calc_Bragg_angle(Energy).subs(Sub.structure.subs).evalf())
angle=pl.linspace(0.975, 1.006,501)*thBragg
""" Cut of Reciprocal Space Outer Batch file for pyasf.py. Written by Carsten Richter ([email protected]) """ import itertools import pylab as pl import pyasf import time mydict = dict({"Abs":abs}) cs = pyasf.unit_cell("MyBaseFileName_9837.cif") cs.get_tensor_symmetry() cs.build_unit_cell() energy = 10000. ha = pl.linspace(-2, 2, 801)*10 la = pl.linspace(-2, 2, 801)*10 Imap = 0 * ha * la[:,pl.newaxis] cs.calc_structure_factor() I0 = abs(cs.DAFS(energy, (0,0,0), force_refresh=False))**2 def gaussian(x, x0, amp, w, y0=0): return amp*pl.exp(-(x-x0)**2/(2*w**2))+y0
data = pl.loadtxt("sto_m28_ez_8_myt1_norm.dat")
R = 0, 0, 2
xmax = 25
strainmax = 0.0106
t = .62 * 1e4
x = np.linspace(0, xmax, 101)
strain = (strainmax * np.exp(-x) * (1 + x))[::-1]
strain = np.delete(strain, 0)
tvector = (x * t)
#pl.plot(tvector[1:], strain[::-1])
#pl.show()
Energy = 8000
structsub = pyasf.unit_cell("1507756") #BaTiO3
structsub.subs[structsub.a] = 3.9064
structsub.subs[structsub.c] = 3.9064
Sub = reflectivity.Substrate(structsub)
struct1 = pyasf.unit_cell("1507756")
struct1.subs[struct1.a] = 3.9064
struct1.subs[struct1.c] = 3.9064
layer1 = reflectivity.Strained_Layer(struct1, tvector, c=strain)
psi = 0
v_perp = sp.Matrix([0, 0, 1])
Sub.calc_orientation_from_angle(psi, v_perp)
layer1.calc_orientation_from_angle(psi, v_perp)
crystal = reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
data = pl.loadtxt("test6.dat")
data[:, 0] = pl.radians(data[:, 0])
#pl.ion()
R = 1, 1, 3
thickness = 1000
Energy = 10000
#struct = pyasf.unit_cell("1011117")
struct = pyasf.unit_cell("cif/MgO_52026.cif") #MgO
Sub = reflectivity.Substrate(struct)
v_par = sp.Matrix([1, -1, 0])
v_perp = sp.Matrix([1, 1, 0])
Sub.calc_orientation(v_par, v_perp)
layer1 = reflectivity.Epitaxial_Layer(struct, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal = reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg = float(
layer1.calc_Bragg_angle(Energy).subs(layer1.structure.subs).evalf())
angle = pl.linspace(0.995, 1.005, 501) * thBragg
crystal.calc_reflectivity(angle, Energy)
layer1.calc_amplitudes(angle, Energy)
import os
#os.chdir(os.path.expanduser("~/Desktop/reflectivity/dynXRD/"))
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
import numpy as np
# Substrate
structsub = pyasf.unit_cell("9008845") #GaAs
Sub=reflectivity.Substrate(structsub)
# Strained layers
struct1=pyasf.unit_cell("9008845") #GaAs
tvector=np.array([0, 3, 4.5, 5.5, 6])*1e4
strain=np.array([20, 15, 10, 5])*1e-4
layer1=reflectivity.Strained_Layer(struct1, tvector, a=strain)
# Geometry of substrate and layers
psi=0
v_perp=sp.Matrix([0,0,1])
Sub.calc_orientation_from_angle(psi, v_perp)
layer1.calc_orientation_from_angle(psi, v_perp)
# Crystal sample
crystal=reflectivity.Sample(Sub, layer1)
# Miller indices
R = 0,0,4
crystal.set_Miller(R)
import os
import pyasf
import reflectivity
import sympy as sp
import pylab as pl
import numpy as np
R = 0,0,4
thickness=np.array([3, 1.5, 1, 0.5])*1e4
strain=np.array([20, 15, 10, 5])*1e-4
Energy=8048
structsub = pyasf.unit_cell("9008845") #GaAs
Sub=reflectivity.Substrate(structsub)
Layers=[]
for i in range(4):
layer=reflectivity.Epitaxial_Layer(pyasf.unit_cell("9008845"), thickness[i])
Layers.append(layer)
Layers[i].structure.subs[Layers[i].structure.a]*=(1+strain[i])
psi=0
v_perp=sp.Matrix([0,0,1])
Sub.calc_orientation_from_angle(psi, v_perp)
for i in range(4):
Layers[i].calc_orientation_from_angle(psi, v_perp)