"""
Atomic form factor f0 calculations (legacy module, use xoppy_calc_f0 instead).
"""
#
# file to be removed: copied to xoppy_calc_f0 (for uniformity)
#
import numpy
from dabax.common_tools import calculate_f0_from_f0coeff, atomic_number, atomic_symbols
from dabax.dabax_xraylib import DabaxXraylib
try: import xraylib
except: pass
[docs]def f0_calc(
MAT_FLAG,
DESCRIPTOR,
GRIDSTART,
GRIDEND,
GRIDN,
FILE_NAME="",
charge=0.0,
material_constants_library=None,
):
qscale = numpy.linspace(GRIDSTART, GRIDEND, GRIDN)
f0 = numpy.zeros_like(qscale)
if MAT_FLAG == 0: # element
descriptor = DESCRIPTOR
# for i,iqscale in enumerate(qscale):
Z = atomic_number(descriptor)
if isinstance(material_constants_library, DabaxXraylib):
coeffs = material_constants_library.f0_with_fractional_charge(Z, charge=charge)
f0 = calculate_f0_from_f0coeff(coeffs, qscale)
else:
for i in range(qscale.size):
f0[i] = material_constants_library.FF_Rayl(Z, qscale[i])
elif MAT_FLAG == 1: # formula
tmp = material_constants_library.CompoundParser(DESCRIPTOR)
zetas = tmp["Elements"]
multiplicity = tmp["nAtoms"]
if isinstance(material_constants_library, DabaxXraylib):
for j ,jz in enumerate(zetas):
coeffs = material_constants_library.f0_with_fractional_charge(jz, charge=charge)
f0 += multiplicity[j] * calculate_f0_from_f0coeff(coeffs, qscale)
else:
if charge != 0:
raise Exception(NotImplementedError)
for i in range(qscale.size):
for j, jz in enumerate(zetas):
f0[i] += multiplicity[j] * material_constants_library.FF_Rayl(jz, qscale[i])
elif MAT_FLAG == 2: # nist
if isinstance(material_constants_library, DabaxXraylib):
raise Exception(NotImplementedError) # TODO: implement
else:
Zarray = material_constants_library.GetCompoundDataNISTByName(DESCRIPTOR)
zetas = Zarray["Elements"]
fractions = numpy.array(Zarray["massFractions"])
multiplicity = []
for i in range(fractions.size):
Z = zetas[i]
multiplicity.append( fractions[i] / material_constants_library.AtomicWeight(Z) )
multiplicity = numpy.array(multiplicity)
multiplicity /= multiplicity.min()
atwt = 0.0
for i in range(fractions.size):
Z = zetas[i]
atwt += multiplicity[i] * material_constants_library.AtomicWeight(Z)
print("f0_calc - nist: ")
print(" Descriptor: ", DESCRIPTOR)
print(" Zs: ", zetas)
print(" n: ", multiplicity)
print(" atomic weight: ", atwt)
for i in range(qscale.size):
for j, jz in enumerate(zetas):
f0[i] += multiplicity[j] * material_constants_library.FF_Rayl(jz, qscale[i])
else:
raise Exception("Not implemented")
if FILE_NAME != "":
with open(FILE_NAME, "w") as file:
try:
file.write("#F %s\n " %FILE_NAME)
file.write("\n#S 1 xoppy f0 results\n")
file.write("#N 2\n")
file.write("#L q=sin(theta)/lambda [A^-1] f0 [electron units]\n")
for j in range(qscale.size):
# file.write("%19.12e "%energy[j])
file.write("%19.12e %19.12e\n " %(qscale[j] ,f0[j]))
file.close()
print("File written to disk: %s \n " %FILE_NAME)
except:
raise Exception("f0: The data could not be dumped onto the specified file!\n")
#
# return
#
return {"application" :"xoppy" ,"name" :"f0" ,"data" :numpy.vstack((qscale ,f0))
,"labels" :["q=sin(theta)/lambda [A^-1]" ,"f0 [electron units]"]}
if __name__ == "__main__":
dx = DabaxXraylib()
Si_xrl = f0_calc(0, "Si", 0, 6, 100, material_constants_library=xraylib)
Si_dbx = f0_calc(0, "Si", 0, 6, 100, material_constants_library=dx)
H2O_xrl = f0_calc(1, "H2O", 0, 6, 100, material_constants_library=xraylib)
H2O_dbx = f0_calc(1, "H2O", 0, 6, 100, material_constants_library=dx)
#
# H2O_xrl = XraylibDecorated.f0_calc(2, "Water, Liquid", 0, 6, 100)
# H2O_dbx = DabaxDecorated.f0_calc(2, "Water, Liquid", 0, 6, 100)
#
from srxraylib.plot.gol import plot
plot(Si_xrl["data"][0, :], Si_xrl["data"][1, :],
Si_dbx["data"][0, :], Si_dbx["data"][1, :],
H2O_xrl["data"][0, :], H2O_xrl["data"][1, :],
H2O_dbx["data"][0, :], H2O_dbx["data"][1, :],
linestyle=[None, '', None, ''],
marker=[None, '+', None, '+'],
color=['r', 'r', 'b', 'b'],
legend=['Si xraylib', 'Si dabax', 'H2O xraylib', 'H2O dabax'])