def surface_check():
func = double_diamond
cube = cube_lattice(lattice_num=70, flambda=func)
delt = 0.1
cube_d = (np.abs(cube)<delt).astype(float)
plt.imshow(cube_d[:,:,-1])
plt.colorbar()
plt.show()
qsvec, intens_str = straight_intensity(cube_d, peakmax=5)
lenqs = qsvec_to_lenqs(qsvec)
intens_str /= (intens_str*lenqs*lenqs).sum()
intens_mod = np.load("../data/dd_model_surf.npy")
intens_paper = np.load("../data/dd_paper_surf.npy")
plt.title("DD")
plt.plot(lenqs,intens_mod,'bo',label="surface appr")
plt.plot(lenqs, intens_str,'^g', label="direct surface")
plt.plot(lenqs, intens_paper,'r+',label="paper data")
#for x in range(len(qsvec)):
# print x, qsvec[x]
cube_b = ((cube)<0).astype(float)
qsvec, intens_bulk = straight_intensity(cube_b, peakmax=5)
intens_bulk /= (intens_bulk*lenqs*lenqs).sum()
plt.plot(lenqs, intens_bulk,'xk', label="direct bulk")
plt.legend()
plt.show()
plt.imshow(cube_b[:,:,-1])
plt.colorbar()
plt.show()
def test_by_sin(npoints=100):
s = lambda x, y, z: np.sin(2*np.pi*4*r(x,y,z))
sizelat = 4
l = sizelat/2
r = lambda x, y, z: np.sqrt((x-l)**2 + (y-l)**2 + (z-l)**2)
cube = cube_lattice(lattice_num=npoints, flambda=s, sizelat=sizelat)
plt.imshow(cube[npoints/2, :,:])
plt.colorbar()
plt.show()
cube -= np.average(cube)
peakmax = 10.
lenqs2, intens_mod = straight_intensity(cube, peakmax=peakmax, sizelat=sizelat)
intens_mod /= lenqs2**2
plt.plot(lenqs2, intens_mod,'--b')
plt.plot(lenqs2, intens_mod,'bo')
plt.title("ФП в точках, ячеек:{}".format(sizelat))
plt.ylabel("I, a.u.")
plt.xlabel("q, a.u.")
plt.show()
output(name="test3", pic_path=".", lenqs=lenqs2, intens_exp=intens_mod,
intens_mod=intens_mod, error=0., xaxis=np.array([0.,9.]))
from Fourier import fourier_base
lenqs_f, intens_f = fourier_base(cube)
lenqs_f /= sizelat
plt.plot(lenqs_f, intens_f/np.max(intens_f),'-r')
plt.title("Полное ФП, ячеек:{}".format(sizelat))
plt.ylabel("I, a.u.")
plt.xlabel("q, a.u.")
plt.show()
def diamond_symmetry(con):
N = 100
pm = 4
tr = 0.05
sizelat = 1
func = double_diamond
cubezero = double_sign_lattice(lattice_num=N, func=func, con=con, sizelat=sizelat)
print round(cubezero.sum()/N**3,3)
cubezero /= cubezero.sum()
qsvec, intens_zero = straight_intensity(cubezero, peakmax=pm, sizelat=sizelat)
_, lenqs = generate_qvecs_lenqs_deprecated(peakmax=pm)
plt.plot(lenqs, intens_zero, 'bo')
plt.plot(lenqs, intens_zero, '--g')
for num, x in enumerate(qsvec):
if intens_zero[num]>tr:
print x, round(lenqs[num],3)
plt.title(con)
plt.show()
slice = cubezero[0, :, :]
plt.imshow(slice)
plt.colorbar()
plt.show()
def diamond_paper_res():
peakmax = 6
qsvec, lenqs = generate_qvecs_lenqs_deprecated(peakmax)
func_p = lambda x, y, z: double_diamond(x, y, z, const=0)
gart_list = np.array([0.]*len(qsvec))#len(qsvec))
"""
#gyr
gart_list[5] = 0.65
gart_list[6] = 0.43
gart_list[12] = 0.097
gart_list[13] = 0.34
gart_list[17] = 0.33
gart_list[19] = 0.47
gart_list[20] = 0.27
gart_list[22] = 0.189
gart_list[30] = 0.41
"""
for num, q in enumerate(qsvec):
print num, q
#dd
gart_list[6] = 0.958
gart_list[10] = 0.97
gart_list[13] = 0.523
gart_list[20] = 0.424
gart_list[26] = 0.516
#gart_list[30] = 0.56
qsvec_new, intens_paper = calc_model_set_fstruct(gart_list, 0.05, ddens=1., peakmax=peakmax)
intens_paper /= (intens_paper*lenqs*lenqs).sum()
sizelat = 1.
intenses = []
Ns = [30, 110]
for N in Ns:
#print N
cube_p = cube_lattice(N, func_p, sizelat=sizelat)
qsvec, lenqs = generate_qvecs_lenqs_deprecated(peakmax)
factor_struct = factor_calc_structural(qsvec, cube_p)
#print factor_struct
qsvec_new, intens_mod = calc_model_set_fstruct(factor_struct, layer=0.05, ddens=1., peakmax=peakmax)
print max(intens_mod)
intens_mod /= (intens_mod*lenqs*lenqs).sum()
print max(intens_mod)
print
intenses.append(intens_mod)
#plt.plot(lenqs, intens_mod,'o',label='m surface %d'%(N))
plt.plot(lenqs, intens_paper, '^', label='external data')
plt.title("DD")
cube_n = cube_lattice(80, func_p, sizelat=sizelat)
for err in [0.20]:
cube_p = (cube_n<0)#err
qsvec, intens_dir = straight_intensity(lattice=cube_p, peakmax=peakmax,sizelat=sizelat)
intens_dir /= (intens_dir*lenqs*lenqs).sum()
print ((intens_dir - intens_paper)**2).sum()
plt.plot(lenqs, intens_dir,"s", label="m direct {:1.3f}".format((cube_p>0).astype(float).sum()/80**3))
cube_p = (np.abs(cube_n)<err)
qsvec, intens_dir = straight_intensity(lattice=cube_p, peakmax=peakmax, sizelat=sizelat)
intens_dir /= (intens_dir*lenqs*lenqs).sum()
print ((intens_dir - intens_paper)**2).sum()
plt.plot(lenqs, intens_dir,"s", label="m direct surf {:1.3f}, {:1.3f}".format((cube_p>0).astype(float).sum()/80**3, err))
plt.legend(bbox_to_anchor=(0.8, 1.1))
#up = np.sqrt(((intens_paper-intens_mod)**2).sum())
#down1 = np.sqrt((intens_paper**2).sum())
#down2 = np.sqrt((intens_mod**2).sum())
#print down1, down2
#print up/down1, up/down2
#plt.show()
#diff = intens_paper/intens_mod
#diff = diff[np.nonzero(diff)]
plt.show()
plt.imshow(cube_p[0,:,:])
plt.show()
np.save("../data/dd_model_surf.npy", intenses[0])
def single_point(*args):
try:
mkdir(addr)
except:
pass
if args is not ():
phi1 = args[0]
phi2 = args[1]
rho_abs_h20, rho_abs_pol, rho_abs_alk = args[2]
val_debye = args[3]
else:
global phi1, phi2, rho_abs_h20
global rho_abs_pol, rho_abs_alk, val_debye
print(phi1, phi2, (rho_abs_h20,rho_abs_pol, rho_abs_alk), val_debye)
qsvec, lenqs = generate_qvecs_lenqs(peakmax=lenqsmax)
#experimental data correction
lenqs_exp_grand, intens_exp_grand = read_exp_data(scat_exp_file, intens_exp_file)
peaks_indices = find_peaks_ind_in_smooth_profile(intens_exp_grand, cond='>')
lenqs_exp = lenqs_exp_grand[peaks_indices]
intens_exp = intens_exp_grand[peaks_indices]
lattice_parameter = get_lattice_parameter(lenqs_exp_abs=lenqs_exp, peaks_file=peaks_file)
print("lattice parameter: {:1.3f}".format(1./lattice_parameter))
lenqs_exp /= lattice_parameter
lenqs_exp_grand /= lattice_parameter
lenqs_exp = peaks_file_to_lenqs(peaks_file)
exp_ind_in_model = find_exp_indices(lenqs_exp_short=lenqs_exp, lenqs_model=lenqs, corr_file=peaks_file) #corrction of model
intens_exp = insert_exp_peaks(intensity_exp=intens_exp, indices_exp=exp_ind_in_model, lenqs_model=lenqs)
#for model correction
ind_forbid = []
peak_max = exp_ind_in_model[-1]
print("inices higher than {} ({}) are forbidden".format(peak_max, qsvec[peak_max]))
if qsvec_forbid is not None:
ind_forbid = find_indices(qsvec_forbid, lenqs)
print("hkl forbid: {}, ind forbid{}:".format(str(qsvec_forbid), ind_forbid))
#for output xaxis
ind_exp = np.nonzero(intens_exp)[0]
xaxis = [round(lenqs[ind_exp[0]])-1, round(lenqs[ind_exp[-1]])+1]
#init
lenqs = qsvec_to_lenqs(qsvec)
#brute force
con1 = phi_to_const(phi1)
cube_in = build_lattice_function(lattice_num=lattice_num, func=model_function, con=con1, warn=global_warn, sizelat=sizelat)
con2 = phi_to_const(phi2+phi1)
cube_out = build_lattice_function(lattice_num=lattice_num, func=model_function, con=con2, warn=global_warn, sizelat=sizelat)
cube = (1.-cube_out)*rho_abs_alk
cube += (cube_out - cube_in)*rho_abs_pol
cube += cube_in*rho_abs_h20
print(rho_abs_alk, rho_abs_pol, rho_abs_h20)
plt.title(u"Электронная плотность в срезе")
plt.imshow(cube[0], extent=[0,1,0,1])
plt.colorbar()
plt.show()
cube -= cube.sum()/lattice_num**3
lenqs2, intens_mod = straight_intensity(cube, peakmax=lenqsmax, sizelat=sizelat)
assert lenqs.all()==lenqs2.all(),'trouble!'
debye_factor = np.exp(-(lenqs*val_debye)**2)
intens_mod *= debye_factor
intens_mod[peak_max+1::] = 0.0
intens_mod[ind_forbid] = 0.0
err = calculate_error(lenqs, intens_mod, lenqs, intens_exp, norm='area')
name_cur = "$\phi={}; $\phi2={}, rho=({},{},{}), d={}$".format(phi1, phi2,
rho_abs_h20,rho_abs_pol,rho_abs_alk, val_debye)
output(name=name_cur,pic_path=addr, lenqs=lenqs, intens_exp=intens_exp, intens_mod=intens_mod,
error=err, lenqs_exp_grand=lenqs_exp_grand, intens_exp_grand=intens_exp_grand, xaxis=xaxis)