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 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)