def get_structure_factor(cif_file, dfout=0, **sf_args):
'''computes structure factor 3D
- sf_args : see (structure_factor3D)
returns :
- (qx,qy,qz),Fhkl
'''
crys = import_crys(cif_file)
pattern = np.array([
np.hstack([a.coords_fractional, a.atomic_number]) for a in crys.atoms
])
lat_vec = np.array(crys.reciprocal_vectors)
(h, k, l), Fhkl = structure_factor3D(pattern, lat_vec, **sf_args)
qx = h / crys.lattice_parameters[0]
qy = k / crys.lattice_parameters[1]
qz = l / crys.lattice_parameters[2]
if dfout:
data = [
h.flatten(),
k.flatten(),
l.flatten(),
qx.flatten(),
qy.flatten(),
qz.flatten(),
Fhkl.flatten()
]
d = dict(zip(['h', 'k', 'l', 'qx', 'qy', 'qz', 'Fhkl'], data))
return pd.DataFrame.from_dict(d)
else:
return (qx, qy, qz), Fhkl
def update_Nmax(self, Nmax):
'''Update resolution/max order. (Updates lattice and Fhkl)
Nmax : maximum h,k,l order
'''
if isinstance(Nmax, int):
if not Nmax == self.Nmax:
self.Nmax = Nmax
(h, k, l), (qx, qy,
qz) = mut.get_lattice(self.lat_vec, self.Nmax)
self.lattice = [(h, k, l), (qx, qy, qz)]
self.hklF, self.Fhkl = sf.structure_factor3D(
self.pattern,
2 * np.pi * self.lat_vec,
hklMax=2 * self.Nmax)
def get_pattern(name, N=1, opt='', **kwargs):
# crys = Crystal.from_database(name)
# lat_vec = crys.reciprocal_vectors
# pattern = np.array([list(a.coords_fractional)+[a.atomic_number] for a in crys.atoms])
pptype, ax, by, cz, angle = 'p1', 2, 2, 2, 90
pattern = np.array([[1, 1, 1, 1]])
lat_vec = 2 * np.pi * np.diag([1 / ax, 1 / by, 1 / cz])
hkl, Fhkl = sf.structure_factor3D(pattern, lat_vec, hklMax=2 * N, sym=1)
if opt: sFact.plot_structure3D(hkl, Fhkl, opt=opt, **kwargs)
a, b, c = lat_vec
hkl = np.array(
[i[N:3 * N + 1, N:3 * N + 1, N:3 * N + 1].flatten() for i in hkl])
#hkl = hkl[0].flatten(),hkl[1].flatten(),hkl[2].flatten()])
h, k, l = hkl
kx = a[0] * h + b[0] * k + c[0] * l
ky = a[1] * h + b[1] * k + c[1] * l
kz = a[2] * h + b[2] * k + c[2] * l
Gs = np.array([kx, ky, kz]).T / (2 * np.pi)
Vg = Fhkl #.flatten()
return hkl.T, Gs, Vg / (ax * by * cz)
if 'B' in opts:
df = pd.read_pickle(path+'df0.pkl')
p1 = pp.load_multi_obj(path+'biotin_m0_autoslic.pkl')
p1.datpath = p1.datpath.replace('ronan','tarik')
p1.get_beams(bOpt='na')
#plot
iBs = ['(64,0)','(0,32)','(0,64)','(32,32)','(64,64)']
fig,ax = p1.beam_vs_thickness(iBs=iBs,cm='jet',
fonts=fs,opt='ps',name=figpath+'biotin_m0_beams.png')
if 'F' in opts:
# structure factor
lat_vec = crys.reciprocal_vectors
pattern = np.array([ np.hstack([a.coords_cartesian,a.atomic_number]) for a in crys.atoms])
hkl,F3d = structure_factor3D(pattern,lat_vec,hkl=None,hklMax=3,sym=0)
#excitation error
K = 1/cst.keV2lam(200)
k = [2/a1,2/a2, b12, 2*b12]
ti = np.arcsin(k/K)
xi = K*(1-np.cos(ti))
z = np.linspace(0,2000,2000)
Fibs = F3d[[2,0,0,1,2],[0,1,2,1,2],0]
Fi = [Fibs[i]*np.sin(np.pi*z*zeta_i)/(np.pi*zeta_i) for i,zeta_i in enumerate(xi)]
Ii = np.abs(Fi)**2
#plot kinematic
cs = dsp.getCs('jet',len(iBs))
plts = [[z,I/1e8,[cs[i],'--'],''] for i,I in enumerate(Ii)]
dsp.pltPlots(ax,plts,2)
fig.show()
import importlib as imp
from utils import *
from crystals import Crystal
from scattering import structure_factor as sf
imp.reload(sf)
crys = Crystal.from_database('Si')
pattern = np.array([
np.hstack([a.coords_fractional, 0 * a.atomic_number]) for a in crys.atoms
])
lat_vec = np.array(crys.reciprocal_vectors)
hkl, Fhkl = sf.structure_factor3D(pattern,
lat_vec,
hkl=None,
hklMax=2,
sym=0,
v='')
h, k, l = hkl
I = np.abs(Fhkl)**2
id0 = ~((h % 2 == 0) & (k % 2 == 0) &
(l % 2 == 0)) & ~((h % 2 == 1) & (k % 2 == 1) & (l % 2 == 1))
print(np.abs(I[id0])) #should be 0
print(np.abs(I[~id0 & ((h + k + l) % 4 == 0)])) #should be 64
print(np.abs(I[~id0 & ((h + k + l) % 2 == 1)])) #should be 32
print(np.abs(I[~id0 & ((h + k + l) % 4 == 2)])) #should be 0