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 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 build_nested_lattice_gyroid(lattice_num, con1, con2, dens_in_slash_out=1, flag_apart=False):
"""
:param con1: less constant, bigger gyr
:param con2: bigger constant, smaller gyr
:param dens_in_slash_out: density inside smaller gyr/density outside smaller but inside bigger gyr
:param lattice_num: size of one side
:param flag_apart: if True, returns (cube with inner gyr, cube with outer gyr)
:return: density lattice
"""
if con1 > con2:
C_max = con1
else:
C_max = con2
C_min = con1 + con2 - C_max
# positive
f_cube = lambda x, y, z: gyroid(x, y, z, C_min)
cube_bigger_p = (cube_lattice(lattice_num=lattice_num, flambda=f_cube) < 0).astype(float)
f_cube = lambda x, y, z: gyroid(x, y, z, C_max)
cube_smaller_p = ((cube_lattice(lattice_num=lattice_num, flambda=f_cube)) < 0).astype(float)
cube_positive = cube_smaller_p * dens_in_slash_out
cube_positive += np.logical_xor(cube_bigger_p.astype(bool), cube_smaller_p.astype(bool)).astype(float)
# negative
f_cube = lambda x, y, z: gyroid(x, y, z, -C_min)
cube_bigger_n = (cube_lattice(lattice_num=lattice_num, flambda=f_cube) > 0).astype(float)
f_cube = lambda x, y, z: gyroid(x, y, z, -C_max)
cube_smaller_n = ((cube_lattice(lattice_num=lattice_num, flambda=f_cube)) > 0).astype(float)
cube_negative = cube_smaller_n * dens_in_slash_out
cube_negative += np.logical_xor(cube_bigger_n.astype(bool), cube_smaller_n.astype(bool)).astype(float)
if flag_apart:
return cube_smaller_n + cube_smaller_p, cube_bigger_n + cube_bigger_p
cube = cube_positive + cube_negative
"""
plt.imshow(cube[0])
plt.colorbar()
plt.show()
"""
return cube
def single_sign_lattice(lattice_num, func, con):
"""
returns cube with double structure, +-C
:param lattice_num: size of one side
:param con: constant of structure
:param func: function(x, y, z), when < 0 defines structure
:return: lattice
"""
f_cube_positive = lambda x, y, z: func(x, y, z, con)
cube = cube_lattice(lattice_num=lattice_num, flambda=f_cube_positive) < 0
cube = cube.astype(float)
return cube
def double_sign_lattice(lattice_num, func, con, warn=True, sizelat=1.0):
"""
returns cube with double structure, +-C
:param lattice_num: size of one side
:param con: constant of structure
:param func: function(x, y, z), when < 0 defines structure
:return: lattice
"""
f_cube_positive = lambda x, y, z: func(x, y, z, con)
cube_pos = cube_lattice(lattice_num=lattice_num, flambda=f_cube_positive, sizelat=sizelat) < 0
cube_pos = cube_pos.astype(float)
f_cube_negative = lambda x, y, z: -func(x, y, z, -con)
cube_neg = cube_lattice(lattice_num=lattice_num, flambda=f_cube_negative, sizelat=sizelat) < 0
cube_neg = cube_neg.astype(float)
if cube_neg.sum() != cube_pos.sum() and warn:
mes = "Positive and negative lattices are different: {}, {} ".format(
cube_neg.sum() / lattice_num ** 3, cube_pos.sum() / lattice_num ** 3
)
warnings.warn(mes, RuntimeWarning)
cube = cube_neg + cube_pos
return cube
def build_spheres(filname, radi=0.05, numb=50, flagshow=False):
coords = take_coord(filname)
if flagshow:
show_coord(coords)
rsphere = lambda x,y,z,x0,y0,z0: _sphere( x, y, z, x0, y0, z0, r=radi)
cube = np.zeros((numb, numb, numb)) + 1.
print(cube.sum()/numb**3)
for point in coords:
p=point
f = lambda x, y, z: rsphere(x,y,z,x0=p[0], y0=p[1], z0=p[2])
cube *= cube_lattice(numb, f).astype(float)
cube -= 1
cube *= -1
print (cube.sum()/numb**3)
plt.imshow(cube[0])
plt.colorbar()
plt.show()
q, i = fourier_base(cube, dimension=1)
plt.plot(q, i)
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])
def research_diamond():
interp_func = double_diamond
save_interpolate = False
const_pnum = 100
N = 50
fit_degree = 6
bounds_const = (0.7, 1.4)
const_s = np.linspace(bounds_const[0], bounds_const[1], const_pnum)
phi_s = np.zeros((len(const_s)))
phi = lambda cube: float((cube>0).sum())/N**3
"""
for num, con in enumerate(const_s):
ff = lambda x,y,z: double_diamond(x,y,z, const=con)
cube = cube_lattice(flambda=ff, lattice_num=N)
ff = lambda x,y,z: -double_diamond(x,y,z, const=-con)
cube2 = cube_lattice(flambda=ff, lattice_num=N)
triangulate_and_show_cube(cube)
triangulate_and_show_cube(cube2, color='r')
cube *= cube2
triangulate_and_show_cube(cube, color='g')
"""
n = 61
c = cube_lattice(lattice_num=n, flambda=interp_func)
c = (c>0).astype(float)
print c.sum()*2,n**3
for num, con in enumerate(const_s):
cube = double_sign_lattice(lattice_num=N, func=interp_func, con=con, warn=False)
print con, cube.sum()/N**3
if num%10==0:
pass
#triangulate_and_show_cube(cube)
phi_s[num] = phi(cube)
interp = np.polyfit(phi_s, const_s, fit_degree)
def res_inter(x):
res = 0
N = len(interp)
extents = range(N)
for num in extents:
res += interp[num]*x**(N-1-num)
return res
interp_const = res_inter(phi_s)
interp = np.around(interp, decimals=3)
plt.plot(phi_s, const_s, 'xr', label="data")
plt.plot(phi_s, interp_const,'-g', label="interpolation")
plt.xlabel("$\phi$")
plt.ylabel("C(const)")
name = "diamond half C="
N = len(interp)
extents = range(N)
countsize = len(name)
threshold = 40
for num in extents:
if num!=0:
temp = "%+.2f"%(interp[num])
else:
temp = "%.2f"%(interp[num])
if (N-1-num)!=0:
temp+=("${\phi}^{%d}$" % (N-1-num))
name += temp
countsize += len(temp)
if countsize>threshold:
countsize = 0
name +='\n'
name += '\n'+'error:'+"%.3g"%(((interp_const-const_s)**2).sum()/(const_s**2).sum())
phi_s_red = phi_s[phi_s<0.2]
plt.plot(phi_s, phi_to_const_double_double_diam(phi_s), '--b', label="function")
plt.title(name)
plt.legend(loc=3)
plt.tight_layout()
cube_test = single_sign_lattice(lattice_num=N, func=_diamond, con=1.087)
print (cube_test.sum())/N**3
plt.show()
if save_interpolate:
f = open("inter_res.py", 'w')