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 factor_calc_molecular(qsvec, layer, ddens, alph=1):
"""
:param qsvec: 3d scattering vector
:param layer: width of layer
:param alph: 'podgon' coefficient
:param ddens: delta density up/down the surface
:return: molecular(form) factor in qvec point(or qvec points) for polygonized surface
"""
t = qsvec.shape
assert t[len(t)-1] == 3, "Molecular factor needs qsvec"
lenqs = 2*np.pi* qsvec_to_lenqs(qsvec)
factor = ddens* 2./lenqs * np.sin(alph * lenqs * layer/2.)
return factor
def factor_calc_structural(qsvec, cube):
"""
:param qsvec: 3d scattering vector or vectors
:param cube: cubic mesh with values of implicit surface
:return: structural factor for given qsvec
"""
t = qsvec.shape
assert t[len(t)-1] == 3, "Structural factor needs qsvec"
rvec, surfvec = center_area_cube(cube)
qsvec_local = deepcopy(qsvec)
qsvec_local = qsvec_local.transpose()
try:
lensurf = qsvec_to_lenqs(surfvec)
except:
print(len(surfvec))
raise ValueError()
exponent = np.dot(rvec, 2*np.pi*qsvec_local)
sf = np.dot(lensurf, np.exp(1j*exponent))
return np.abs(sf)
def task_surface():
try:
mkdir(addr)
except:
pass
#parameter space generation
qsvec, lenqs = generate_qvecs_lenqs_deprecated(peakmax=peakmax)
const_s = np.linspace(bounds_const[0], bounds_const[-1], pnum_const)
layer_s = np.linspace(bounds_const[0], bounds_const[-1], pnum_layer)
#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)
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]
if qsvec_forbid is not None:
ind_forbid = find_indices(qsvec_forbid, lenqs)
print("ind forbid: "+str(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
err_map = np.zeros((pnum_const, pnum_layer))
lenqs = qsvec_to_lenqs(qsvec)
#brute_force
for num_const, val_const in enumerate(const_s):
func_p = lambda x, y, z: double_diamond(x, y, z, const=val_const)
cube_p = cube_lattice(lattice_num, func_p)
func_n = lambda x, y, z: -double_diamond(x, y, z, const=-val_const)
cube_n = cube_lattice(lattice_num, func_n)
factor_struct = factor_calc_structural(qsvec, cube_p*cube_n)
for num_layer, val_layer in enumerate(layer_s):
temp_intens_exp = deepcopy(intens_exp)
qsvec_new, intens_mod = calc_model_set_fstruct(factor_struct, val_layer, ddens=1., peakmax=peakmax)
assert (qsvec_new == qsvec).prod(), "Something went wrong with qsvec's "
err = calculate_error(lenqs, intens_mod, lenqs, temp_intens_exp, norm='area')
err_map[num_const, num_layer] = err
if err<errtr:
assert (temp_intens_exp/max(temp_intens_exp)).all() == (intens_exp/max(intens_exp)).all(),"intens was changed during err calc"
name_cur = "p1(%1.2f) p2(%1.2f) " % (val_const, val_layer)
output(name=name_cur,pic_path=addr, lenqs=lenqs, intens_exp=temp_intens_exp, intens_mod=intens_mod,
error=err, lenqs_exp_grand=lenqs_exp_grand, intens_exp_grand=intens_exp_grand, xaxis=xaxis)
np.save(addr+'/'+model_name+"results.npy", err_map)
parameters = np.array([const_s, layer_s])
np.save(addr+'/'+model_name+"params.npy", parameters)
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)
