def calc_model_full(func_no_const, lattice_num, layer=0.1, const=0.0, ddens=1, peakmax=5):
"""
:param func_no_const: function that sets the surface implicitly
:param lattice_num: points in one side of mesh
:param layer: layer width, fraction of lattice parameter
:param const: const for function
:param peakmax: max number in hkl
:param show: to show or not to show triangulation
:return:
"""
def func(x, y, z):
return func_no_const(x, y, z, const)
qsvec, lenqs = generate_qvecs_lenqs_deprecated(peakmax)
cube = cube_lattice(lattice_num, func)
factor_struct = factor_calc_structural(qsvec, cube)
factor_mol = factor_calc_molecular(qsvec, layer, ddens)
amplitude = factor_struct * factor_mol
intensity = amplitude**2
multiplicity = factor_calc_multiplicity_intens(qsvec)
intensity *= multiplicity
lorentz = lenqs * lenqs
intensity *= lorentz
return qsvec, intensity
def calc_model_set_fstruct_doublelayer(factor_structural, layer_in, ddens_in, layer_out, ddens_out, peakmax=5):
assert layer_in <= layer_out, 'layer out should be greater or equal than layer in'
qsvec, lenqs = generate_qvecs_lenqs_deprecated(peakmax)
multipl = factor_calc_multiplicity_intens(qsvec)
if len(factor_structural) != len(qsvec):
raise ValueError("different size of struct factor and number of peaks")
#
factor_molecular = factor_calc_molecular(qsvec, layer_in, ddens_in-ddens_out)\
+ factor_calc_molecular(qsvec, layer_out, ddens_out)
#
amplitude = factor_structural * factor_molecular
intensity = amplitude**2 * np.array(multipl) * lenqs**2
return qsvec, intensity
def calc_model_set_fstruct(factor_structural, layer, ddens, peakmax=5):
"""
:param factor_structural: preset structural factor for all points
:param layer: width of layer, fraction of lattice parameter
:param peakmax: max number in hkl
:return: qsvec, intensity
"""
qsvec, lenqs = generate_qvecs_lenqs_deprecated(peakmax)
multipl = factor_calc_multiplicity_intens(qsvec)
if len(factor_structural) != len(qsvec):
raise ValueError("different size of struct factor and number of peaks")
#
factor_molecular = factor_calc_molecular(qsvec, layer, ddens)
#
amplitude = factor_structural * factor_molecular
intensity = amplitude**2 * np.array(multipl) * lenqs**2
return qsvec, intensity
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 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 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])