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 _straight_intensity_v2(lattice, peakmax=5):
qsvec, lenqs = generate_qvecs_lenqs_full(peakmax)
lattice_num = len(lattice)
x, y, z = np.mgrid[:1:lattice_num * 1j, :1:lattice_num * 1j, :1:lattice_num * 1j]
intensity = []
for m in range(len(qsvec)):
qvec = qsvec[m]
fexp = lambda x, y, z: np.exp(1j * 2 * np.pi * (x * qvec[0] + y * qvec[1] + z * qvec[2]))
cuber = fexp(x, y, z) * lattice
intensity.append((np.abs(cuber.sum())).astype(float)**2)
intensity = np.array(intensity)
intensity *= lenqs**2*factor_calc_multiplicity_intens(qsvec)
intensity /= max(intensity)
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 straight_intensity(lattice, peakmax=5, sizelat=1):
qsvec, lenqs = generate_qvecs_lenqs_full(peakmax, uniquelenq=False)
lattice_num = len(lattice)
x, y, z = np.mgrid[:sizelat:lattice_num * 1j, :sizelat:lattice_num * 1j, :sizelat:lattice_num * 1j]
intensity = []
for m in range(len(qsvec)):
qvec = qsvec[m]
qC = x*qvec[0] + y*qvec[1] + z*qvec[2]
expqC = np.exp(2*np.pi*1j*qC)
amplitude = np.abs((expqC*lattice).sum()).astype(float)
#print(lenqs[m], np.abs(amplitude))
intensity.append((amplitude*lenqs[m])**2)
intensity = np.array(intensity)
intensity *= factor_calc_multiplicity_intens(qsvec)
lenqs, intensity = filter_unique(np.round(lenqs,4), intensity, concat=True)
intensity /= max(intensity)
return lenqs, 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
