def xoppy_calc_xcrystal(self):
CRYSTAL_MATERIAL = self.CRYSTAL_MATERIAL
MILLER_INDEX_H = self.MILLER_INDEX_H
MILLER_INDEX_K = self.MILLER_INDEX_K
MILLER_INDEX_L = self.MILLER_INDEX_L
TEMPER = self.TEMPER
MOSAIC = self.MOSAIC
GEOMETRY = self.GEOMETRY
SCAN = self.SCAN
UNIT = self.UNIT
SCANFROM = self.SCANFROM
SCANTO = self.SCANTO
SCANPOINTS = self.SCANPOINTS
ENERGY = self.ENERGY
ASYMMETRY_ANGLE = self.ASYMMETRY_ANGLE
THICKNESS = self.THICKNESS
MOSAIC_FWHM = self.MOSAIC_FWHM
RSAG = self.RSAG
RMER = self.RMER
ANISOTROPY = self.ANISOTROPY
POISSON = self.POISSON
CUT = self.CUT
FILECOMPLIANCE = self.FILECOMPLIANCE
for file in ["diff_pat.dat","diff_pat.gle","diff_pat.par","diff_pat.xop","xcrystal.bra"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
if (GEOMETRY == 1) or (GEOMETRY == 3):
if ASYMMETRY_ANGLE == 0.0:
print("xoppy_calc_xcrystal: WARNING: In xcrystal the asymmetry angle is the angle between Bragg planes and crystal surface,"+
"in BOTH Bragg and Laue geometries.")
descriptor = Crystal_GetCrystalsList()[CRYSTAL_MATERIAL]
if SCAN == 3: # energy scan
emin = SCANFROM - 1
emax = SCANTO + 1
else:
emin = ENERGY - 100.0
emax = ENERGY + 100.0
print("Using crystal descriptor: ",descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=MILLER_INDEX_H,kk=MILLER_INDEX_K,ll=MILLER_INDEX_L,
temper=float(TEMPER),
emin=emin,emax=emax,estep=5.0,fileout="xcrystal.bra")
with open("xoppy.inp", "wt") as f:
f.write("xcrystal.bra\n")
f.write("%d\n"%MOSAIC)
f.write("%d\n"%GEOMETRY)
if MOSAIC == 1:
f.write("%g\n"%MOSAIC_FWHM)
f.write("%g\n"%THICKNESS)
else:
f.write("%g\n"%THICKNESS)
f.write("%g\n"%ASYMMETRY_ANGLE)
scan_flag = 1 + SCAN
f.write("%d\n"%scan_flag)
f.write("%19.9f\n"%ENERGY)
if scan_flag <= 3:
f.write("%d\n"%UNIT)
f.write("%g\n"%SCANFROM)
f.write("%g\n"%SCANTO)
f.write("%d\n"%SCANPOINTS)
if MOSAIC > 1: # bent
f.write("%g\n"%RSAG)
f.write("%g\n"%RMER)
f.write("0\n")
if ( (descriptor == "Si") or (descriptor == "Si2") or (descriptor == "Si_NIST") or (descriptor == "Ge") or descriptor == "Diamond"):
pass
else: # not Si,Ge,Diamond
if ((ANISOTROPY == 1) or (ANISOTROPY == 2)):
raise Exception("Anisotropy data not available for this crystal. Either use isotropic or use external compliance file. Please change and run again'")
f.write("%d\n"%ANISOTROPY)
if ANISOTROPY == 0:
f.write("%g\n"%POISSON)
elif ANISOTROPY == 1:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
f.write("%d\n"%MILLER_INDEX_H)
f.write("%d\n"%MILLER_INDEX_K)
f.write("%d\n"%MILLER_INDEX_L)
elif ANISOTROPY == 2:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
# TODO: check syntax for CUT: Cut syntax is: valong_X valong_Y valong_Z ; vnorm_X vnorm_Y vnorm_Z ; vperp_x vperp_Y vperp_Z
f.write("%s\n"%CUT.split(";")[0])
f.write("%s\n"%CUT.split(";")[1])
f.write("%s\n"%CUT.split(";")[2])
elif ANISOTROPY == 3:
f.write("%s\n"%FILECOMPLIANCE)
command = "'" + os.path.join(locations.home_bin(), 'diff_pat') + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#show calculated parameters in standard output
txt_info = open("diff_pat.par").read()
for line in txt_info:
print(line,end="")
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("diff_pat.dat", skiprows=5))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
calculated_data.add_content("units_to_degrees", self.get_units_to_degrees())
except Exception as e:
raise Exception("Error loading diff_pat.dat :" + str(e))
try:
calculated_data.add_content("labels",
["Th-ThB{in} [" + self.unit_combo.itemText(self.UNIT) + "]",
"Th-ThB{out} [" + self.unit_combo.itemText(self.UNIT) + "]",
"phase_p[rad]",
"phase_s[rad]","Circ Polariz",
"p-polarized reflectivity",
"s-polarized reflectivity"])
except:
pass
try:
with open("diff_pat.par") as f:
info = f.readlines()
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def xoppy_calc_xfh(self):
#TODO: remove I_ABSORP
ILATTICE = self.ILATTICE
HMILLER = self.HMILLER
KMILLER = self.KMILLER
LMILLER = self.LMILLER
I_PLOT = self.I_PLOT
TEMPER = self.TEMPER
ENERGY = self.ENERGY
ENERGY_END = self.ENERGY_END
NPOINTS = self.NPOINTS
descriptor = Crystal_GetCrystalsList()[ILATTICE]
print("Using crystal descriptor: ", descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=HMILLER,
kk=KMILLER,
ll=LMILLER,
temper=TEMPER,
emin=ENERGY,
emax=ENERGY_END,
estep=50.0,
fileout=None)
energy = numpy.linspace(ENERGY, ENERGY_END, NPOINTS)
out = numpy.zeros((25, NPOINTS))
info = ""
for i, ienergy in enumerate(energy):
dic2 = crystal_fh(bragg_dictionary, ienergy)
print("Energy=%g eV FH=(%g,%g)" %
(ienergy, dic2["STRUCT"].real, dic2["STRUCT"].imag))
out[0, i] = ienergy
out[1, i] = dic2["WAVELENGTH"] * 1e10
out[2, i] = dic2["THETA"] * 180 / numpy.pi
out[3, i] = dic2["F_0"].real
out[4, i] = dic2["F_0"].imag
out[5, i] = dic2["FH"].real
out[6, i] = dic2["FH"].imag
out[7, i] = dic2["FH_BAR"].real
out[8, i] = dic2["FH_BAR"].imag
out[9, i] = dic2["psi_0"].real
out[10, i] = dic2["psi_0"].imag
out[11, i] = dic2["psi_h"].real
out[12, i] = dic2["psi_h"].imag
out[13, i] = dic2["psi_hbar"].real
out[14, i] = dic2["psi_hbar"].imag
out[15, i] = dic2["STRUCT"].real
out[16, i] = dic2["STRUCT"].imag
out[17, i] = dic2["DELTA_REF"]
out[18, i] = dic2["REFRAC"].real
out[19, i] = dic2["REFRAC"].imag
out[20, i] = dic2["ABSORP"]
out[21, i] = 1e6 * dic2["ssr"] # in microrads
out[22, i] = 1e6 * dic2["spr"] # in microrads
out[23, i] = dic2["RATIO"]
out[24, i] = dic2["psi_over_f"]
info += "#\n#\n#\n"
info += dic2["info"]
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out.T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", I_PLOT)
except:
pass
try:
calculated_data.add_content("labels", self.plotOptionList())
except:
pass
try:
calculated_data.add_content("info", info)
except:
pass
if self.DUMP_TO_FILE:
with open(self.FILE_NAME, "w") as file:
try:
file.write("#F %s\n" % self.FILE_NAME)
file.write("\n#S 1 xoppy CrossSec results\n")
file.write("#N %d\n" % (out.shape[0]))
tmp = "#L"
for item in self.plotOptionList():
tmp += " %s" % (item)
tmp += "\n"
file.write(tmp)
for j in range(out.shape[1]):
file.write(
("%19.12e " * out.shape[0] + "\n") %
tuple(out[i, j] for i in range(out.shape[0])))
file.close()
print("File written to disk: %s \n" % self.FILE_NAME)
except:
raise Exception(
"CrossSec: The data could not be dumped onto the specified file!\n"
)
return calculated_data
def xoppy_calc_xcrystal(self):
CRYSTAL_MATERIAL = self.CRYSTAL_MATERIAL
MILLER_INDEX_H = self.MILLER_INDEX_H
MILLER_INDEX_K = self.MILLER_INDEX_K
MILLER_INDEX_L = self.MILLER_INDEX_L
TEMPER = self.TEMPER
MOSAIC = self.MOSAIC
GEOMETRY = self.GEOMETRY
SCAN = self.SCAN
UNIT = self.UNIT
SCANFROM = self.SCANFROM
SCANTO = self.SCANTO
SCANPOINTS = self.SCANPOINTS
ENERGY = self.ENERGY
ASYMMETRY_ANGLE = self.ASYMMETRY_ANGLE
THICKNESS = self.THICKNESS
MOSAIC_FWHM = self.MOSAIC_FWHM
RSAG = self.RSAG
RMER = self.RMER
ANISOTROPY = self.ANISOTROPY
POISSON = self.POISSON
CUT = self.CUT
FILECOMPLIANCE = self.FILECOMPLIANCE
for file in ["diff_pat.dat","diff_pat.gle","diff_pat.par","diff_pat.xop","xcrystal.bra"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
if (GEOMETRY == 1) or (GEOMETRY == 3):
if ASYMMETRY_ANGLE == 0.0:
print("xoppy_calc_xcrystal: WARNING: In xcrystal the asymmetry angle is the angle between Bragg planes and crystal surface,"+
"in BOTH Bragg and Laue geometries.")
descriptor = Crystal_GetCrystalsList()[CRYSTAL_MATERIAL]
if SCAN == 3: # energy scan
emin = SCANFROM - 1
emax = SCANTO + 1
else:
emin = ENERGY - 100.0
emax = ENERGY + 100.0
print("Using crystal descriptor: ",descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=MILLER_INDEX_H,kk=MILLER_INDEX_K,ll=MILLER_INDEX_L,
temper=float(TEMPER),
emin=emin,emax=emax,estep=5.0,fileout="xcrystal.bra")
with open("xoppy.inp", "wt") as f:
f.write("xcrystal.bra\n")
f.write("%d\n"%MOSAIC)
f.write("%d\n"%GEOMETRY)
if MOSAIC == 1:
f.write("%g\n"%MOSAIC_FWHM)
f.write("%g\n"%THICKNESS)
else:
f.write("%g\n"%THICKNESS)
f.write("%g\n"%ASYMMETRY_ANGLE)
scan_flag = 1 + SCAN
f.write("%d\n"%scan_flag)
f.write("%19.9f\n"%ENERGY)
if scan_flag <= 3:
f.write("%d\n"%UNIT)
f.write("%g\n"%SCANFROM)
f.write("%g\n"%SCANTO)
f.write("%d\n"%SCANPOINTS)
if MOSAIC > 1: # bent
f.write("%g\n"%RSAG)
f.write("%g\n"%RMER)
f.write("0\n")
if ( (descriptor == "Si") or (descriptor == "Si2") or (descriptor == "Si_NIST") or (descriptor == "Ge") or descriptor == "Diamond"):
pass
else: # not Si,Ge,Diamond
if ((ANISOTROPY == 1) or (ANISOTROPY == 2)):
raise Exception("Anisotropy data not available for this crystal. Either use isotropic or use external compliance file. Please change and run again'")
f.write("%d\n"%ANISOTROPY)
if ANISOTROPY == 0:
f.write("%g\n"%POISSON)
elif ANISOTROPY == 1:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
f.write("%d\n"%MILLER_INDEX_H)
f.write("%d\n"%MILLER_INDEX_K)
f.write("%d\n"%MILLER_INDEX_L)
elif ANISOTROPY == 2:
f.write("%d\n"%CRYSTAL_MATERIAL)
f.write("%g\n"%ASYMMETRY_ANGLE)
# TODO: check syntax for CUT: Cut syntax is: valong_X valong_Y valong_Z ; vnorm_X vnorm_Y vnorm_Z ; vperp_x vperp_Y vperp_Z
f.write("%s\n"%CUT.split(";")[0])
f.write("%s\n"%CUT.split(";")[1])
f.write("%s\n"%CUT.split(";")[2])
elif ANISOTROPY == 3:
f.write("%s\n"%FILECOMPLIANCE)
command = os.path.join(locations.home_bin(), 'diff_pat') + " < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#show calculated parameters in standard output
txt_info = open("diff_pat.par").read()
for line in txt_info:
print(line,end="")
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("diff_pat.dat", skiprows=5))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
calculated_data.add_content("units_to_degrees", self.get_units_to_degrees())
except Exception as e:
raise Exception("Error loading diff_pat.dat :" + str(e))
try:
calculated_data.add_content("labels",
["Th-ThB{in} [" + self.unit_combo.itemText(self.UNIT) + "]",
"Th-ThB{out} [" + self.unit_combo.itemText(self.UNIT) + "]",
"phase_p[rad]",
"phase_s[rad]","Circ Polariz",
"p-polarized reflectivity",
"s-polarized reflectivity"])
except:
pass
try:
with open("diff_pat.par") as f:
info = f.readlines()
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def calculate_with_xoppy(
bragg_or_laue=0, #
diffracted_or_transmitted=0, #
crystal_name="Si", # string
thickness=1e-2, # meters
miller_h=1, # int
miller_k=1, # int
miller_l=1, # int
asymmetry_angle=0.0, # radians
energy=8000.0, # eV
angle_deviation_min=-100e-6, # radians
angle_deviation_max=100e-6, # radians
angle_deviation_points=500,
):
MILLER_INDEX_H = miller_h
MILLER_INDEX_K = miller_k
MILLER_INDEX_L = miller_l
TEMPER = 1.0
MOSAIC = 0
if bragg_or_laue == 0:
if diffracted_or_transmitted == 0:
GEOMETRY = 0
elif diffracted_or_transmitted == 1:
GEOMETRY = 2
else:
raise Exception("Bad geometry type")
elif bragg_or_laue == 1:
if diffracted_or_transmitted == 0:
GEOMETRY = 1
elif diffracted_or_transmitted == 1:
GEOMETRY = 3
else:
raise Exception("Bad geometry type")
else:
raise Exception("Bad geometry type")
SCAN = 2
UNIT = 0 # rad
SCANFROM = angle_deviation_min
SCANTO = angle_deviation_max
SCANPOINTS = angle_deviation_points
ENERGY = energy
ASYMMETRY_ANGLE = asymmetry_angle * 180.0 / numpy.pi
THICKNESS = thickness * 100
MOSAIC_FWHM = 0.0
RSAG = 0.0
RMER = 0.0
ANISOTROPY = 0
POISSON = 0.0
CUT = 0
FILECOMPLIANCE = ""
for file in [
"diff_pat.dat", "diff_pat.gle", "diff_pat.par", "diff_pat.xop",
"xcrystal.bra"
]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
if (GEOMETRY == 1) or (GEOMETRY == 3):
if ASYMMETRY_ANGLE == 0.0:
print(
"xoppy_calc_xcrystal: WARNING: In xcrystal the asymmetry angle is the angle between Bragg planes and crystal surface,"
+ "in BOTH Bragg and Laue geometries.")
descriptor = crystal_name
if SCAN == 3: # energy scan
emin = SCANFROM - 1
emax = SCANTO + 1
else:
emin = ENERGY - 100.0
emax = ENERGY + 100.0
print("Using crystal descriptor: ", descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,
hh=MILLER_INDEX_H,
kk=MILLER_INDEX_K,
ll=MILLER_INDEX_L,
temper=float(TEMPER),
emin=emin,
emax=emax,
estep=5.0,
fileout="xcrystal.bra")
with open("xoppy.inp", "wt") as f:
f.write("xcrystal.bra\n")
f.write("%d\n" % MOSAIC)
f.write("%d\n" % GEOMETRY)
if MOSAIC == 1:
f.write("%g\n" % MOSAIC_FWHM)
f.write("%g\n" % THICKNESS)
else:
f.write("%g\n" % THICKNESS)
f.write("%g\n" % ASYMMETRY_ANGLE)
scan_flag = 1 + SCAN
f.write("%d\n" % scan_flag)
f.write("%19.9f\n" % ENERGY)
if scan_flag <= 3:
f.write("%d\n" % UNIT)
f.write("%g\n" % SCANFROM)
f.write("%g\n" % SCANTO)
f.write("%d\n" % SCANPOINTS)
if MOSAIC > 1: # bent
f.write("%g\n" % RSAG)
f.write("%g\n" % RMER)
f.write("0\n")
if ((descriptor == "Si") or (descriptor == "Si2")
or (descriptor == "Si_NIST") or (descriptor == "Ge")
or descriptor == "Diamond"):
pass
else: # not Si,Ge,Diamond
if ((ANISOTROPY == 1) or (ANISOTROPY == 2)):
raise Exception(
"Anisotropy data not available for this crystal. Either use isotropic or use external compliance file. Please change and run again'"
)
f.write("%d\n" % ANISOTROPY)
if ANISOTROPY == 0:
f.write("%g\n" % POISSON)
elif ANISOTROPY == 1:
f.write("%d\n" % CRYSTAL_MATERIAL)
f.write("%g\n" % ASYMMETRY_ANGLE)
f.write("%d\n" % MILLER_INDEX_H)
f.write("%d\n" % MILLER_INDEX_K)
f.write("%d\n" % MILLER_INDEX_L)
elif ANISOTROPY == 2:
f.write("%d\n" % CRYSTAL_MATERIAL)
f.write("%g\n" % ASYMMETRY_ANGLE)
# TODO: check syntax for CUT: Cut syntax is: valong_X valong_Y valong_Z ; vnorm_X vnorm_Y vnorm_Z ; vperp_x vperp_Y vperp_Z
f.write("%s\n" % CUT.split(";")[0])
f.write("%s\n" % CUT.split(";")[1])
f.write("%s\n" % CUT.split(";")[2])
elif ANISOTROPY == 3:
f.write("%s\n" % FILECOMPLIANCE)
command = os.path.join(locations.home_bin(), 'diff_pat') + " < xoppy.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#show calculated parameters in standard output
txt_info = open("diff_pat.par").read()
for line in txt_info:
print(line, end="")
try:
calculated_data = numpy.loadtxt("diff_pat.dat", skiprows=5)
except Exception as e:
raise Exception("Error loading diff_pat.dat :" + str(e))
print(calculated_data.shape)
deviations = calculated_data[:, 0].copy()
intensityS = calculated_data[:, 6].copy()
intensityP = calculated_data[:, 5].copy()
return deviations, intensityS, intensityP
def xoppy_calc_xfh(self):
#TODO: remove I_ABSORP
ILATTICE = self.ILATTICE
HMILLER = self.HMILLER
KMILLER = self.KMILLER
LMILLER = self.LMILLER
I_PLOT = self.I_PLOT
TEMPER = self.TEMPER
ENERGY = self.ENERGY
ENERGY_END = self.ENERGY_END
NPOINTS = self.NPOINTS
descriptor = Crystal_GetCrystalsList()[ILATTICE]
print("Using crystal descriptor: ",descriptor)
bragg_dictionary = bragg_calc(descriptor=descriptor,hh=HMILLER,kk=KMILLER,ll=LMILLER,temper=TEMPER,
emin=ENERGY,emax=ENERGY_END,estep=50.0,fileout="/dev/null")
energy = numpy.linspace(ENERGY,ENERGY_END,NPOINTS)
out = numpy.zeros((25,NPOINTS))
info = ""
for i,ienergy in enumerate(energy):
dic2 = crystal_fh(bragg_dictionary,ienergy)
print("Energy=%g eV FH=(%g,%g)"%(ienergy,dic2["STRUCT"].real,dic2["STRUCT"].imag))
out[0,i] = ienergy
out[1,i] = dic2["WAVELENGTH"]*1e10
out[2,i] = dic2["THETA"]*180/numpy.pi
out[3,i] = dic2["F_0"].real
out[4,i] = dic2["F_0"].imag
out[5,i] = dic2["FH"].real
out[6,i] = dic2["FH"].imag
out[7,i] = dic2["FH_BAR"].real
out[8,i] = dic2["FH_BAR"].imag
out[9,i] = dic2["psi_0"].real
out[10,i] = dic2["psi_0"].imag
out[11,i] = dic2["psi_h"].real
out[12,i] = dic2["psi_h"].imag
out[13,i] = dic2["psi_hbar"].real
out[14,i] = dic2["psi_hbar"].imag
out[15,i] = dic2["STRUCT"].real
out[16,i] = dic2["STRUCT"].imag
out[17,i] = dic2["DELTA_REF"]
out[18,i] = dic2["REFRAC"].real
out[19,i] = dic2["REFRAC"].imag
out[20,i] = dic2["ABSORP"]
out[21,i] = 1e6 * dic2["ssr"] # in microrads
out[22,i] = 1e6 * dic2["spr"] # in microrads
out[23,i] = dic2["RATIO"]
out[24,i] = dic2["psi_over_f"]
info += "#\n#\n#\n"
info += dic2["info"]
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out.T)
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col", I_PLOT)
except:
pass
try:
calculated_data.add_content("labels",self.plotOptionList())
except:
pass
try:
calculated_data.add_content("info",info)
except:
pass
return calculated_data