def calculateSld(self, event):
"""
Calculate the neutron scattering density length of a molecule
"""
self.clear_outputs()
try:
#Check validity user inputs
flag, msg = self.check_inputs()
if self.base is not None and msg.lstrip().rstrip() != "":
msg = "SLD Calculator: %s" % str(msg)
wx.PostEvent(self.base, StatusEvent(status=msg))
if not flag:
return
#get ready to compute
self.sld_formula = formula(self.compound, density=self.density)
(sld_real, sld_im, _), (_, absorp, incoh), \
length = neutron_scattering(compound=self.compound,
density=self.density,
wavelength=self.neutron_wavelength)
if self.xray_source == "[A]":
energy = xray_energy(self.xray_source_input)
xray_real, xray_im = xray_sld_from_atoms(
self.sld_formula.atoms,
density=self.density,
energy=energy)
elif self.xray_source == "[keV]":
xray_real, xray_im = xray_sld_from_atoms(
self.sld_formula.atoms,
density=self.density,
energy=self.xray_source_input)
elif self.xray_source == "Element":
xray_real, xray_im = self.calculate_sld_helper(
element=self.xray_source_input,
density=self.density,
molecule_formula=self.sld_formula)
# set neutron sld values
val = format_number(sld_real * _SCALE)
self.neutron_sld_real_ctl.SetValue(val)
val = format_number(math.fabs(sld_im) * _SCALE)
self.neutron_sld_im_ctl.SetValue(val)
# Compute the Cu SLD
self.xray_sld_real_ctl.SetValue(format_number(xray_real * _SCALE))
val = format_number(math.fabs(xray_im) * _SCALE)
self.xray_sld_im_ctl.SetValue(val)
# set incoherence and absorption
self.neutron_inc_ctl.SetValue(format_number(incoh))
self.neutron_abs_ctl.SetValue(format_number(absorp))
# Neutron length
self.neutron_length_ctl.SetValue(format_number(length))
# display wavelength
#self.wavelength_ctl.SetValue(str(self.wavelength))
#self.wavelength_ctl.SetValue(str(self.wavelength))
except:
if self.base is not None:
msg = "SLD Calculator: %s" % (sys.exc_value)
wx.PostEvent(self.base, StatusEvent(status=msg))
if event is not None:
event.Skip()
def calculateSld(self, event):
"""
Calculate the neutron scattering density length of a molecule
"""
self.clear_outputs()
try:
#Check validity user inputs
flag, msg = self.check_inputs()
if self.base is not None and msg.lstrip().rstrip() != "":
msg = "SLD Calculator: %s" % str(msg)
wx.PostEvent(self.base, StatusEvent(status=msg))
if not flag:
return
#get ready to compute
self.sld_formula = formula(self.compound,
density=self.density)
(sld_real, sld_im, _), (_, absorp, incoh), \
length = neutron_scattering(compound=self.compound,
density=self.density,
wavelength=self.neutron_wavelength)
if self.xray_source == "[A]":
energy = xray_energy(self.xray_source_input)
xray_real, xray_im = xray_sld_from_atoms(self.sld_formula.atoms,
density=self.density,
energy=energy)
elif self.xray_source == "[keV]":
xray_real, xray_im = xray_sld_from_atoms(self.sld_formula.atoms,
density=self.density,
energy=self.xray_source_input)
elif self.xray_source == "Element":
xray_real, xray_im = self.calculate_sld_helper(element=self.xray_source_input,
density=self.density,
molecule_formula=self.sld_formula)
# set neutron sld values
val = format_number(sld_real * _SCALE)
self.neutron_sld_real_ctl.SetValue(val)
val = format_number(math.fabs(sld_im) * _SCALE)
self.neutron_sld_im_ctl.SetValue(val)
# Compute the Cu SLD
self.xray_sld_real_ctl.SetValue(format_number(xray_real * _SCALE))
val = format_number(math.fabs(xray_im) * _SCALE)
self.xray_sld_im_ctl.SetValue(val)
# set incoherence and absorption
self.neutron_inc_ctl.SetValue(format_number(incoh))
self.neutron_abs_ctl.SetValue(format_number(absorp))
# Neutron length
self.neutron_length_ctl.SetValue(format_number(length))
# display wavelength
#self.wavelength_ctl.SetValue(str(self.wavelength))
#self.wavelength_ctl.SetValue(str(self.wavelength))
except:
if self.base is not None:
msg = "SLD Calculator: %s" % (sys.exc_value)
wx.PostEvent(self.base, StatusEvent(status=msg))
if event is not None:
event.Skip()
def calculate_xray_sld(element, density, molecule_formula):
"""
Get an element and compute the corresponding SLD for a given formula
:param element: elements a string of existing atom
"""
element_formula = formula(str(element))
if len(element_formula.atoms) != 1:
return
element = element_formula.atoms.keys()[0]
energy = xray_energy(element.K_alpha)
atom = molecule_formula.atoms
return xray_sld_from_atoms(atom, density=density, energy=energy)
def calculate_xray_sld(element, density, molecule_formula):
"""
Get an element and compute the corresponding SLD for a given formula
:param element: elements a string of existing atom
"""
element_formula = formula(str(element))
if len(element_formula.atoms) != 1:
return
element = next(iter(element_formula.atoms)) # only one element...
energy = xray_energy(element.K_alpha)
atom = molecule_formula.atoms
return xray_sld_from_atoms(atom, density=density, energy=energy)
def calculate_sld_helper(self, element, density, molecule_formula):
"""
Get an element and compute the corresponding SLD for a given formula
:param element: elements a string of existing atom
"""
element_formula = formula(str(element))
if len(element_formula.atoms) != 1:
return
element = element_formula.atoms.keys()[0]
energy = xray_energy(element.K_alpha)
atom = molecule_formula.atoms
return xray_sld_from_atoms(atom, density=density, energy=energy)
def calculate_xray_sld(self, element):
"""
Get an element and compute the corresponding SLD for a given formula
:param element: elements a string of existing atom
"""
myformula = formula(str(element))
if len(myformula.atoms) != 1:
return
element = myformula.atoms.keys()[0]
energy = xray_energy(element.K_alpha)
self.sld_formula = formula(str(self.compound), density=self.density)
atom = self.sld_formula.atoms
return xray_sld_from_atoms(atom, density=self.density, energy=energy)
def calculate_xray_sld(self, element):
"""
Get an element and compute the corresponding SLD for a given formula
:param element: elements a string of existing atom
"""
myformula = formula(str(element))
if len(myformula.atoms) != 1:
return
element = myformula.atoms.keys()[0]
energy = xray_energy(element.K_alpha)
self.sld_formula = formula(str(self.compound), density=self.density)
atom = self.sld_formula.atoms
return xray_sld_from_atoms(atom, density=self.density, energy=energy)
def calculate_xray_sld(self, element):
"""
Get an element and compute the corresponding SLD for a given formula
:param element: elements a string of existing atom
"""
# TODO: use periodictable.elements object
# energy = xray_energy(periodictable.elements[element].K_alpha)
# TODO: code is very similar to sld helper
myformula = formula(str(element))
if len(myformula.atoms) != 1:
return
element = list(myformula.atoms.keys())[0]
energy = xray_energy(element.K_alpha)
self.sld_formula = formula(str(self.compound), density=self.density)
atom = self.sld_formula.atoms
return xray_sld_from_atoms(atom, density=self.density, energy=energy)
