def xoppy_calc_xtube_w(VOLTAGE=100.0, RIPPLE=0.0, AL_FILTER=0.0):
print("Inside xoppy_calc_xtube_w. ")
for file in ["tasmip_tmp.dat"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
try:
with open("xoppy.inp", "wt") as f:
f.write("%f\n%f\n%f\n" % (VOLTAGE, RIPPLE, AL_FILTER))
if platform.system() == "Windows":
command = "\"" + os.path.join(locations.home_bin(),
'tasmip.exe\" < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(),
'tasmip') + "' < xoppy.inp"
print("Running command '%s' in directory: %s \n" %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
return "tasmip_tmp.dat"
except Exception as e:
raise e
def xoppy_calc_xtube_w(VOLTAGE=100.0,RIPPLE=0.0,AL_FILTER=0.0):
print("Inside xoppy_calc_xtube_w. ")
for file in ["tasmip_tmp.dat"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
try:
with open("xoppy.inp","wt") as f:
f.write("%f\n%f\n%f\n"%(VOLTAGE,RIPPLE,AL_FILTER))
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),'tasmip.exe < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(), 'tasmip') + "' < xoppy.inp"
print("Running command '%s' in directory: %s \n"%(command,locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
return "tasmip_tmp.dat"
except Exception as e:
raise e
def xoppy_calc_xtubes(ITUBE=0, VOLTAGE=30.0):
print("Inside xoppy_calc_xtubes. ")
for file in ["xtubes_tmp.dat"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
try:
with open("xoppy.inp", "wt") as f:
f.write("%d\n%f\n" % (ITUBE + 1, VOLTAGE))
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),
'xtubes.exe < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(),
"xtubes") + "' < xoppy.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
return os.path.join(locations.home_bin_run(), "xtubes_tmp.dat")
except Exception as e:
raise e
def xoppy_calc_xtubes(ITUBE=0,VOLTAGE=30.0):
print("Inside xoppy_calc_xtubes. ")
for file in ["xtubes_tmp.dat"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
try:
with open("xoppy.inp","wt") as f:
f.write("%d\n%f\n"%(ITUBE+1,VOLTAGE))
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),'xtubes.exe < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(), "xtubes") + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
return os.path.join(locations.home_bin_run(), "xtubes_tmp.dat")
except Exception as e:
raise e
def xoppy_calc_ws(ENERGY=7.0,CUR=100.0,PERIOD=8.5,N=28.0,KX=0.0,KY=8.739999771118164,\
EMIN=1000.0,EMAX=100000.0,NEE=2000,D=30.0,XPC=0.0,YPC=0.0,XPS=2.0,YPS=2.0,NXP=10,NYP=10):
print("Inside xoppy_calc_ws. ")
try:
with open("ws.inp", "wt") as f:
f.write("inputs from xoppy \n")
f.write("%f %f\n" % (ENERGY, CUR))
f.write("%f %d %f %f\n" % (PERIOD, N, KX, KY))
f.write("%f %f %d\n" % (EMIN, EMAX, NEE))
f.write("%f %f %f %f %f %d %d\n" %
(D, XPC, YPC, XPS, YPS, NXP, NYP))
f.write("%d \n" % (4))
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(), 'ws.exe')
else:
command = "'" + os.path.join(locations.home_bin(), 'ws') + "'"
print("Running command '%s' in directory: %s \n" %
(command, locations.home_bin_run()))
# TODO try to capture the text output of the external code
os.system(command)
# write spec file
txt = open("ws.out").readlines()
outFile = os.path.join(locations.home_bin_run(), "ws.spec")
f = open(outFile, "w")
f.write("#F ws.spec\n")
f.write("\n")
f.write("#S 1 ws results\n")
f.write("#N 4\n")
f.write(
"#L Energy(eV) Flux(photons/s/0.1%bw) Spectral power(W/eV) Cumulated power(W)\n"
)
cum = 0.0
estep = (EMAX - EMIN) / (NEE - 1)
for i in txt:
tmp = i.strip(" ")
if tmp[0].isdigit():
tmp1 = numpy.fromstring(tmp, dtype=float, sep=' ')
cum += tmp1[1] * codata.e * 1e3
f.write(
"%f %g %f %f \n" %
(tmp1[0], tmp1[1], tmp1[1] * codata.e * 1e3, cum * estep))
else:
f.write("#UD " + tmp)
f.close()
print("File written to disk: ws.spec")
# print output file
# for line in txt:
# print(line, end="")
print("Results written to file: %s" %
os.path.join(locations.home_bin_run(), 'ws.out'))
return outFile
except Exception as e:
raise e
def xoppy_calc_xpowder_fml(self):
for file in ["xpowder_fml.par","xpowder_fml.ref","xpowder_fml.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("xoppy.inp", "wt") as f:
f.write("%s\n"% (self.FILE))
f.write("%s\n"%(self.TITLE))
f.write("%g\n"%(self.LAMBDA))
f.write("%s\n"%(self.JOB))
f.write("%g\n"%(self.U))
f.write("%g\n"%(self.V))
f.write("%g\n"%(self.W))
f.write("%g\n"%(self.X))
f.write("%g\n"%(self.LS))
f.write("%g\n"%(self.THMIN))
f.write("%g\n"%(self.STEP))
f.write("%s\n"%(self.THMAX))
if platform.system() == "Windows":
command = "\"" + os.path.join(locations.home_bin(),'xpowder_fml.exe\" < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(), 'xpowder_fml') + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
print("Files written to disk:\n xpowder_fml.par (text output)\n xpowder_fml.ref (reflections)\n xpowder_fml.out (diffractogram)",)
#
# data = numpy.loadtxt("xpowder_fml.out",skiprows=3).T
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("xpowder_fml.out", skiprows=3))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
except:
pass
try:
calculated_data.add_content("labels",["TwoTheta[Deg]","Intensity[a.u.]"])
except:
pass
try:
with open("xpowder_fml.par") as f:
info = f.readlines()
info = [line[:-1] for line in info] # remove "\n"
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def xoppy_calc_xpowder_fml(self):
for file in ["xpowder_fml.par","xpowder_fml.ref","xpowder_fml.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("xoppy.inp", "wt") as f:
f.write("%s\n"% (self.FILE))
f.write("%s\n"%(self.TITLE))
f.write("%g\n"%(self.LAMBDA))
f.write("%s\n"%(self.JOB))
f.write("%g\n"%(self.U))
f.write("%g\n"%(self.V))
f.write("%g\n"%(self.W))
f.write("%g\n"%(self.X))
f.write("%g\n"%(self.LS))
f.write("%g\n"%(self.THMIN))
f.write("%g\n"%(self.STEP))
f.write("%s\n"%(self.THMAX))
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),'xpowder_fml.exe < xoppy.inp')
else:
command = "'" + os.path.join(locations.home_bin(), 'xpowder_fml') + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
print("Files written to disk:\n xpowder_fml.par (text output)\n xpowder_fml.ref (reflections)\n xpowder_fml.out (diffractogram)",)
#
# data = numpy.loadtxt("xpowder_fml.out",skiprows=3).T
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("xpowder_fml.out", skiprows=3))
calculated_data.add_content("plot_x_col",0)
calculated_data.add_content("plot_y_col",-1)
except:
pass
try:
calculated_data.add_content("labels",["TwoTheta[Deg]","Intensity[a.u.]"])
except:
pass
try:
with open("xpowder_fml.par") as f:
info = f.readlines()
info = [line[:-1] for line in info] # remove "\n"
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def xoppy_calc_ws(ENERGY=7.0,CUR=100.0,PERIOD=8.5,N=28.0,KX=0.0,KY=8.739999771118164,\
EMIN=1000.0,EMAX=100000.0,NEE=2000,D=30.0,XPC=0.0,YPC=0.0,XPS=2.0,YPS=2.0,NXP=10,NYP=10):
print("Inside xoppy_calc_ws. ")
try:
with open("ws.inp","wt") as f:
f.write("inputs from xoppy \n")
f.write("%f %f\n"%(ENERGY,CUR))
f.write("%f %d %f %f\n"%(PERIOD,N,KX,KY))
f.write("%f %f %d\n"%(EMIN,EMAX,NEE))
f.write("%f %f %f %f %f %d %d\n"%(D,XPC,YPC,XPS,YPS,NXP,NYP))
f.write("%d \n"%(4))
command = os.path.join(locations.home_bin(),'ws')
print("Running command '%s' in directory: %s \n"%(command, locations.home_bin_run()))
# TODO try to capture the text output of the external code
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
# write spec file
txt = open("ws.out").readlines()
outFile = os.path.join(locations.home_bin_run(), "ws.spec")
f = open(outFile,"w")
f.write("#F ws.spec\n")
f.write("\n")
f.write("#S 1 ws results\n")
f.write("#N 3\n")
f.write("#L Energy(eV) Flux(photons/s/0.1%bw) Spectral power(W/eV)\n")
for i in txt:
tmp = i.strip(" ")
if tmp[0].isdigit():
tmp1 = numpy.fromstring(tmp, dtype=float, sep=' ')
f.write("%f %f %f \n"%(tmp1[0],tmp1[1],tmp1[1]*codata.e*1e3))
else:
f.write("#UD "+tmp)
f.close()
print("File written to disk: ws.spec")
# print output file
for line in txt:
print(line, end="")
return outFile
except Exception as e:
raise e
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_mlayer(self):
# copy the variable locally, so no more use of self.
MODE = self.MODE
SCAN = self.SCAN
F12_FLAG = self.F12_FLAG
SUBSTRATE = self.SUBSTRATE
ODD_MATERIAL = self.ODD_MATERIAL
EVEN_MATERIAL = self.EVEN_MATERIAL
ENERGY = self.ENERGY
THETA = self.THETA
SCAN_STEP = self.SCAN_STEP
NPOINTS = self.NPOINTS
ODD_THICKNESS = self.ODD_THICKNESS
EVEN_THICKNESS = self.EVEN_THICKNESS
NLAYERS = self.NLAYERS
FILE = self.FILE
for file in ["mlayer.inp", "mlayer.par", "mlayer.f12"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
#
# write input file for Fortran mlayer: mlayer.inp
#
f = open('mlayer.inp', 'w')
if SCAN == 0 and MODE == 0: a0 = 1
if SCAN == 1 and MODE == 0: a0 = 2
if SCAN == 0 and MODE == 1: a0 = 3
if SCAN == 1 and MODE == 1: a0 = 4
f.write("%d \n" % a0)
f.write("N\n")
f.write("%g\n" % (codata.h * codata.c / codata.e * 1e10 / ENERGY))
f.write("%g\n" % THETA)
#
if SCAN == 0:
f.write("%g\n" % SCAN_STEP)
a2 = codata.h * codata.c / codata.e * 1e10 / ENERGY
a3 = codata.h * codata.c / codata.e * 1e10 / (ENERGY + SCAN_STEP)
a4 = a3 - a2
if SCAN != 0:
f.write("%g\n" % a4)
#
f.write("%d\n" % NPOINTS)
if MODE == 0:
f.write("%d\n" % NLAYERS)
if MODE == 0:
if a0 != 5:
f.write("%g %g \n" % (ODD_THICKNESS, EVEN_THICKNESS))
else:
for i in range(NLAYERS):
f.write("%g %g \n" % (ODD_THICKNESS, EVEN_THICKNESS))
if MODE != 0:
f1 = open(FILE, 'r')
a5 = f1.read()
f1.close()
if MODE != 0:
print("Number of layers in %s file is %d " % (FILE, NLAYERS))
f.write("%d\n" % NLAYERS)
f.write(a5)
f.write("mlayer.par\n")
f.write("mlayer.dat\n")
f.write("6\n")
f.close()
print('File written to disk: mlayer.inp')
#
# create f12 file
#
if F12_FLAG == 0:
energy = numpy.arange(0, 500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
f12_s = f1f2_calc(SUBSTRATE, energy)
f12_e = f1f2_calc(EVEN_MATERIAL, energy)
f12_o = f1f2_calc(ODD_MATERIAL, energy)
f = open("mlayer.f12", 'w')
f.write(
'; File created by xoppy for materials [substrate=%s,even=%s,odd=%s]: \n'
% (SUBSTRATE, EVEN_MATERIAL, ODD_MATERIAL))
f.write('; Atomic masses: \n')
f.write(
"%g %g %g \n" %
(xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.AtomicWeight(
xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.AtomicWeight(
xraylib.SymbolToAtomicNumber(ODD_MATERIAL))))
f.write('; Densities: \n')
f.write("%g %g %g \n" %
(xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(ODD_MATERIAL))))
f.write('; Number of energy points: \n')
f.write("%d\n" % (energy.size))
f.write(
'; For each energy point, energy[eV], f1[substrate], f2[substrate], f1[even], f2[even], f1[odd], f2[odd]: \n'
)
for i in range(energy.size):
f.write("%g %g %g %g %g %g %g \n" %
(energy[i], f12_s[0, i], f12_s[1, i], f12_e[0, i],
f12_e[1, i], f12_o[0, i], f12_o[1, i]))
f.close()
print('File written to disk: mlayer.f12')
#
# run external program mlayer
#
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),
'mlayer.exe < mlayer.inp')
else:
command = "'" + os.path.join(locations.home_bin(),
'mlayer') + "' < mlayer.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
if SCAN == 0:
calculated_data.add_content("xoppy_data",
numpy.loadtxt("mlayer.dat"))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 3)
elif SCAN == 1: # internal scan is in wavelength. Add a column with energy
aa = numpy.loadtxt("mlayer.dat")
photon_energy = (codata.h * codata.c / codata.e * 1e10) / aa[:,
0]
bb = numpy.zeros((aa.shape[0], 1 + aa.shape[1]))
bb[:, 0] = photon_energy
bb[:, 1:] = aa
calculated_data.add_content("xoppy_data", bb)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 4)
calculated_data.add_content("units_to_degrees", 1.0)
except:
pass
try:
info = "ML %s(%3.2f A):%s(%3.2f A) %d pairs; E=%5.3f eV" % (
ODD_MATERIAL, ODD_THICKNESS, EVEN_MATERIAL, EVEN_THICKNESS,
NLAYERS, ENERGY)
calculated_data.add_content("info", info)
except:
pass
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 xoppy_calc_xtc(self):
for file in ["tc.inp", "tc.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
with open("tc.inp", "wt") as f:
f.write("TS called from xoppy\n")
f.write("%10.3f %10.2f %10.6f %s\n" %
(self.ENERGY, self.CURRENT, self.ENERGY_SPREAD,
"Ring-Energy(GeV) Current(mA) Beam-Energy-Spread"))
f.write("%10.4f %10.4f %10.4f %10.4f %s\n" %
(self.SIGX, self.SIGY, self.SIGX1, self.SIGY1,
"Sx(mm) Sy(mm) Sx1(mrad) Sy1(mrad)"))
f.write("%10.3f %d %s\n" % (self.PERIOD, self.NP, "Period(cm) N"))
f.write("%10.1f %10.1f %d %s\n" %
(self.EMIN, self.EMAX, self.N, "Emin Emax Ne"))
f.write("%d %d %d %s\n" % (self.HARMONIC_FROM, self.HARMONIC_TO,
self.HARMONIC_STEP, "Hmin Hmax Hstep"))
f.write("%d %d %d %d %s\n" %
(self.HELICAL, self.METHOD, 1, self.NEKS,
"Helical Method Print_K Neks"))
f.write("foreground\n")
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(), 'tc.exe')
else:
command = "'" + os.path.join(locations.home_bin(), 'tc') + "'"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("Output file: %s" % ("tc.out"))
print("\n--------------------------------------------------------\n")
#
# parse result files to exchange object
#
with open("tc.out", "r") as f:
lines = f.readlines()
# print output file
# for line in lines:
# print(line, end="")
# remove returns
lines = [line[:-1] for line in lines]
harmonics_data = []
# separate numerical data from text
floatlist = []
harmoniclist = []
txtlist = []
for line in lines:
try:
tmp = line.strip()
if tmp.startswith("Harmonic"):
harmonic_number = int(tmp.split("Harmonic")[1].strip())
if harmonic_number != self.HARMONIC_FROM:
harmonics_data[-1][1] = harmoniclist
harmoniclist = []
harmonics_data.append([harmonic_number, None])
tmp = float(line.strip()[0])
floatlist.append(line)
harmoniclist.append(line)
except:
txtlist.append(line)
harmonics_data[-1][1] = harmoniclist
data = numpy.loadtxt(floatlist)
for index in range(0, len(harmonics_data)):
# print (harmonics_data[index][0], harmonics_data[index][1])
harmonics_data[index][1] = numpy.loadtxt(harmonics_data[index][1])
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 1)
calculated_data.add_content("plot_y_col", 2)
except:
pass
try:
calculated_data.add_content("labels", [
"Energy (eV) without emittance", "Energy (eV) with emittance",
"Brilliance (ph/s/mrad^2/mm^2/0.1%bw)", "Ky",
"Total Power (W)", "Power density (W/mr^2)"
])
except:
pass
try:
calculated_data.add_content("info", txtlist)
except:
pass
return calculated_data
def xoppy_calc_xxcom(
NAME="Pyrex Glass",
SUBSTANCE=3,
DESCRIPTION="SiO2:B2O3:Na2O:Al2O3:K2O",
FRACTION="0.807:0.129:0.038:0.022:0.004",
GRID=1,
GRIDINPUT=0,
GRIDDATA="0.0804:0.2790:0.6616:1.3685:2.7541",
ELEMENTOUTPUT=0,
):
print("Inside xoppy_calc_xxcom. ")
try:
with open("xoppy.inp", "wt") as f:
f.write(os.path.join(locations.home_data(), "xcom") + os.sep + "\n")
f.write(NAME + "\n")
f.write("%d\n" % (1 + SUBSTANCE))
if (1 + SUBSTANCE) != 4:
f.write(DESCRIPTION + "\n")
if (1 + SUBSTANCE) <= 2:
f.write("%d\n" % (1 + ELEMENTOUTPUT))
else:
nn = DESCRIPTION.split(":")
mm = FRACTION.split(":")
f.write("%d\n" % (len(nn)))
for i in range(len(nn)):
f.write(nn[i] + "\n")
f.write(mm[i] + "\n")
f.write("1\n")
f.write("%d\n" % (1 + GRID))
if (1 + GRID) != 1:
f.write("%d\n" % (1 + GRIDINPUT))
if (1 + GRIDINPUT) == 1:
nn = GRIDDATA.split(":")
f.write("%d\n" % (len(nn)))
for i in nn:
f.write(i + "\n")
if (1 + GRID) != 1:
f.write("N\n")
f.write("xcom.out\n")
f.write("1\n")
f.close()
command = os.path.join(locations.home_bin(), "xcom") + " < xoppy.inp"
print("Running command '%s' in directory: %s " % (command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
# write spec file
if (1 + SUBSTANCE) <= 2:
if (1 + ELEMENTOUTPUT) == 1:
titles = (
"Photon Energy [Mev] Coherent scat [b/atom] "
"Incoherent scat [b/atom] Photoel abs [b/atom] "
"Pair prod in nucl field [b/atom] Pair prod in elec field [b/atom] "
"Tot atten with coh scat [b/atom] Tot atten w/o coh scat [b/atom]"
)
elif (1 + ELEMENTOUTPUT) == 2:
titles = (
"Photon Energy [Mev] Coherent scat [b/atom] "
"Incoherent scat [b/atom] Photoel abs [b/atom] "
"Pair prod in nucl field [b/atom] Pair prod in elec field [b/atom] "
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
)
elif (1 + ELEMENTOUTPUT) == 3:
titles = (
"Photon Energy [Mev] Coherent scat [cm2/g] "
"Incoherent scat [cm2/g] Photoel abs [cm2/g] "
"Pair prod in nucl field [cm2/g] Pair prod in elec field [cm2/g] "
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
)
else:
titles = (
"Photon Energy [Mev] Coherent scat [cm2/g] "
"Incoherent scat [cm2/g] Photoel abs [cm2/g] "
"Pair prod in nucl field [cm2/g] Pair prod in elec field [cm2/g] "
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
)
else:
titles = (
"Photon Energy [Mev] Coherent scat [cm2/g] "
"Incoherent scat [cm2/g] Photoel abs [cm2/g] "
"Pair prod in nucl field [cm2/g] Pair prod in elec field [cm2/g] "
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
)
txt = open("xcom.out").readlines()
# copy to standard output
for line in txt:
print(line, end="")
outFile = "xcom.spec"
f = open(outFile, "w")
f.write("#F xcom.spec\n")
f.write("\n")
f.write("#S 1 xcom results\n")
f.write("#N 8\n")
f.write("#L " + titles + "\n")
for i in txt:
tmp = i.strip(" ")
if tmp[0].isdigit():
f.write(tmp)
else:
f.write("#UD " + tmp)
f.close()
print("File written to disk: xcom.spec")
return outFile
except Exception as e:
raise e
def xoppy_calc_xxcom(NAME="Pyrex Glass",SUBSTANCE=3,DESCRIPTION="SiO2:B2O3:Na2O:Al2O3:K2O",\
FRACTION="0.807:0.129:0.038:0.022:0.004",GRID=1,GRIDINPUT=0,\
GRIDDATA="0.0804:0.2790:0.6616:1.3685:2.7541",ELEMENTOUTPUT=0):
print("Inside xoppy_calc_xxcom. ")
try:
with open("xoppy.inp","wt") as f:
f.write(os.path.join(locations.home_data(), 'xcom')+ os.sep + "\n" )
f.write( NAME+"\n" )
f.write("%d\n"%(1+SUBSTANCE))
if (1+SUBSTANCE) != 4:
f.write( DESCRIPTION+"\n")
if (1+SUBSTANCE) <= 2:
f.write("%d\n"%(1+ELEMENTOUTPUT))
else:
nn = DESCRIPTION.split(":")
mm = FRACTION.split(":")
f.write("%d\n"%( len(nn)))
for i in range(len(nn)):
f.write(nn[i]+"\n")
f.write(mm[i]+"\n")
f.write("1\n")
f.write("%d\n"%(1+GRID))
if (1+GRID) != 1:
f.write("%d\n"%(1+GRIDINPUT))
if (1+GRIDINPUT) == 1:
nn = GRIDDATA.split(":")
f.write("%d\n"%( len(nn)))
for i in nn:
f.write(i+"\n")
if (1+GRID) != 1:
f.write("N\n")
f.write("xcom.out\n")
f.write("1\n")
f.close()
command = "'" + os.path.join(locations.home_bin(),'xcom') + "' < xoppy.inp"
print("Running command '%s' in directory: %s "%(command,locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
# write spec file
if (1+SUBSTANCE) <= 2:
if (1+ELEMENTOUTPUT) == 1:
titles = "Photon Energy [Mev] Coherent scat [b/atom] " \
"Incoherent scat [b/atom] Photoel abs [b/atom] " \
"Pair prod in nucl field [b/atom] Pair prod in elec field [b/atom] " \
"Tot atten with coh scat [b/atom] Tot atten w/o coh scat [b/atom]"
elif (1+ELEMENTOUTPUT) == 2:
titles = "Photon Energy [Mev] Coherent scat [b/atom] " \
"Incoherent scat [b/atom] Photoel abs [b/atom] " \
"Pair prod in nucl field [b/atom] Pair prod in elec field [b/atom] " \
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
elif (1+ELEMENTOUTPUT) == 3:
titles = "Photon Energy [Mev] Coherent scat [cm2/g] " \
"Incoherent scat [cm2/g] Photoel abs [cm2/g] " \
"Pair prod in nucl field [cm2/g] Pair prod in elec field [cm2/g] " \
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
else:
titles = "Photon Energy [Mev] Coherent scat [cm2/g] " \
"Incoherent scat [cm2/g] Photoel abs [cm2/g] " \
"Pair prod in nucl field [cm2/g] Pair prod in elec field [cm2/g] " \
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
else:
titles = "Photon Energy [Mev] Coherent scat [cm2/g] " \
"Incoherent scat [cm2/g] Photoel abs [cm2/g] " \
"Pair prod in nucl field [cm2/g] Pair prod in elec field [cm2/g] " \
"Tot atten with coh scat [cm2/g] Tot atten w/o coh scat [cm2/g]"
txt = open("xcom.out").readlines()
# copy to standard output
for line in txt:
print(line,end="")
outFile = "xcom.spec"
f = open(outFile, "w")
f.write("#F xcom.spec\n")
f.write("\n")
f.write("#S 1 xcom results\n")
f.write("#N 8\n")
f.write("#L "+titles+"\n")
for i in txt:
tmp = i.strip(" ")
if tmp[0].isdigit():
f.write(tmp)
else:
f.write("#UD "+tmp)
f.close()
print("File written to disk: xcom.spec")
return outFile
except Exception as e:
raise e
def xoppy_calc_xtcap(self):
for file in ["tcap.inp","tcap.out","tcap.log"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("tcap.inp", "wt") as f:
f.write("TCAP called from xoppy\n")
f.write("%10.3f %10.2f %10.6f %s\n"%(self.ENERGY,self.CURRENT,self.ENERGY_SPREAD,"Ring-Energy(GeV) Current(mA) Beam-Energy-Spread"))
f.write("%10.4f %10.4f %10.4f %10.4f %s\n"%(self.SIGX,self.SIGY,self.SIGX1,self.SIGY1,"Sx(mm) Sy(mm) Sx1(mrad) Sy1(mrad)"))
f.write("%10.3f %d %s\n"%(self.PERIOD,self.NP,"Period(cm) N"))
f.write("%10.1f %10.1f %d %s\n"%(self.EMIN,self.EMAX,self.N,"Emin Emax Ne"))
f.write("%10.3f %10.3f %10.3f %10.3f %10.3f %d %d %s\n"%(self.DISTANCE,self.XPC,self.YPC,self.XPS,self.YPS,10,10,"d xpc ypc xps yps nxp nyp"))
f.write("%d %d %d %d %s\n"%(self.HARMONIC_FROM,self.HARMONIC_TO,self.HARMONIC_STEP,self.HRED,"Hmin Hmax Hstep Hreduction"))
f.write("%d %d %d %d %d %s\n"%(self.HELICAL,self.METHOD,1,self.NEKS,self.BSL,"Helical Method Print_K Neks Bsl-Subtr "))
f.write("foreground\n")
if platform.system() == "Windows":
command = "\"" + os.path.join(locations.home_bin(),'tcap.exe') + "\""
else:
command = "'" + os.path.join(locations.home_bin(), 'tcap') + "'"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
# os.system(command)
#
# catch the optut and write the output to a log file as well as print it.
#
retvalue = os.popen(command).read()
print(retvalue)
with open("tcap.log", "wt") as f:
f.write(retvalue)
print("Output file: '%s/tcap.out'"%(os.getcwd()) )
print("\n--------------------------------------------------------\n")
#
# parse result files to exchange object
#
with open("tcap.out","r") as f:
lines = f.readlines()
# print output file
# for line in lines:
# print(line, end="")
# remove returns
lines = [line[:-1] for line in lines]
harmonics_data = []
# separate numerical data from text
floatlist = []
harmoniclist = []
txtlist = []
for line in lines:
try:
tmp = line.strip()
if tmp.startswith("Harmonic"):
# harmonic_number = int(tmp.split("Harmonic")[1].strip())
harmonic_number = int(tmp.split()[1])
if harmonic_number != self.HARMONIC_FROM:
harmonics_data[-1][1] = harmoniclist
harmoniclist = []
harmonics_data.append([harmonic_number, None])
tmp = float(line.strip()[0])
floatlist.append(line)
harmoniclist.append(line)
except:
txtlist.append(line)
harmonics_data[-1][1] = harmoniclist
data = numpy.loadtxt(floatlist)
for index in range(0, len(harmonics_data)):
# print (harmonics_data[index][0], harmonics_data[index][1])
harmonics_data[index][1] = numpy.loadtxt(harmonics_data[index][1])
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 1)
except:
pass
try:
calculated_data.add_content("labels",["Energy(eV)","Flux(ph/s/0.1%bw)","FWHM(eV)","Ky",
"Ptot(W)","Pd(W/mm^2)","IntP(W)"])
except:
pass
try:
calculated_data.add_content("info",txtlist)
except:
pass
return calculated_data
def xoppy_calc_xinpro(CRYSTAL_MATERIAL=0,MODE=0,ENERGY=8000.0,MILLER_INDEX_H=1,MILLER_INDEX_K=1,MILLER_INDEX_L=1,\
ASYMMETRY_ANGLE=0.0,THICKNESS=500.0,TEMPERATURE=300.0,NPOINTS=100,SCALE=0,XFROM=-50.0,XTO=50.0):
print("Inside xoppy_calc_xinpro. ")
try:
with open("xoppy.inp", "wt") as f:
f.write("%s\n"% (os.path.join(locations.home_data(), "inpro" + os.sep)))
if MODE == 0:
f.write("+1\n")
elif MODE == 1:
f.write("-1\n")
elif MODE == 2:
f.write("+2\n")
elif MODE == 3:
f.write("-1\n")
else:
f.write("ERROR!!\n")
f.write("%f\n%d\n"%(THICKNESS,CRYSTAL_MATERIAL+1))
f.write("%s\n%f\n"%("EV",ENERGY))
f.write("%d\n%d\n%d\n"%(MILLER_INDEX_H,MILLER_INDEX_K,MILLER_INDEX_L))
f.write("%f\n%f\n%s\n"%(ASYMMETRY_ANGLE,TEMPERATURE, "inpro.dat"))
if SCALE == 0:
f.write("1\n")
else:
f.write("%d\n%f\n%f\n"%(2,XFROM,XTO))
f.write("%d\n"%(NPOINTS))
for file in ["inpro.par","inpro.dat","inpro.spec"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
command = os.path.join(locations.home_bin(), 'inpro') + " < xoppy.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#add SPEC header
txt = open("inpro.dat").read()
outFile = "inpro.spec"
f = open(outFile,"w")
f.write("#F inpro.spec\n")
f.write("\n")
f.write("#S 1 inpro results\n")
f.write("#N 3\n")
f.write("#L Theta-TetaB s-polarized reflectivity p-polarized reflectivity\n")
f.write(txt)
f.close()
print("File written to disk: inpro.dat, inpro.par, inpro.spec")
#show calculated parameters in standard output
txt_info = open("inpro.par").read()
for line in txt_info:
print(line,end="")
return outFile
except Exception as e:
raise e
def xoppy_calc_xinpro(CRYSTAL_MATERIAL=0,MODE=0,ENERGY=8000.0,MILLER_INDEX_H=1,MILLER_INDEX_K=1,MILLER_INDEX_L=1,\
ASYMMETRY_ANGLE=0.0,THICKNESS=500.0,TEMPERATURE=300.0,NPOINTS=100,SCALE=0,XFROM=-50.0,XTO=50.0):
print("Inside xoppy_calc_xinpro. ")
try:
with open("xoppy.inp", "wt") as f:
f.write("%s\n" %
(os.path.join(locations.home_data(), "inpro" + os.sep)))
if MODE == 0:
f.write("+1\n")
elif MODE == 1:
f.write("-1\n")
elif MODE == 2:
f.write("+2\n")
elif MODE == 3:
f.write("-1\n")
else:
f.write("ERROR!!\n")
f.write("%f\n%d\n" % (THICKNESS, CRYSTAL_MATERIAL + 1))
f.write("%s\n%f\n" % ("EV", ENERGY))
f.write("%d\n%d\n%d\n" %
(MILLER_INDEX_H, MILLER_INDEX_K, MILLER_INDEX_L))
f.write("%f\n%f\n%s\n" %
(ASYMMETRY_ANGLE, TEMPERATURE, "inpro.dat"))
if SCALE == 0:
f.write("1\n")
else:
f.write("%d\n%f\n%f\n" % (2, XFROM, XTO))
f.write("%d\n" % (NPOINTS))
for file in ["inpro.par", "inpro.dat", "inpro.spec"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
command = "'" + os.path.join(locations.home_bin(),
'inpro') + "' < xoppy.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#add SPEC header
txt = open("inpro.dat").read()
outFile = "inpro.spec"
f = open(outFile, "w")
f.write("#F inpro.spec\n")
f.write("\n")
f.write("#S 1 inpro results\n")
f.write("#N 3\n")
f.write(
"#L Theta-TetaB s-polarized reflectivity p-polarized reflectivity\n"
)
f.write(txt)
f.close()
print("File written to disk: inpro.dat, inpro.par, inpro.spec")
#show calculated parameters in standard output
txt_info = open("inpro.par").read()
for line in txt_info:
print(line, end="")
return outFile
except Exception as e:
raise e
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_xtc(self):
for file in ["tc.inp","tc.out"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
with open("tc.inp", "wt") as f:
f.write("TS called from xoppy\n")
f.write("%10.3f %10.2f %10.6f %s\n"%(self.ENERGY,self.CURRENT,self.ENERGY_SPREAD,"Ring-Energy(GeV) Current(mA) Beam-Energy-Spread"))
f.write("%10.4f %10.4f %10.4f %10.4f %s\n"%(self.SIGX,self.SIGY,self.SIGX1,self.SIGY1,"Sx(mm) Sy(mm) Sx1(mrad) Sy1(mrad)"))
f.write("%10.3f %d %s\n"%(self.PERIOD,self.NP,"Period(cm) N"))
f.write("%10.1f %10.1f %d %s\n"%(self.EMIN,self.EMAX,self.N,"Emin Emax Ne"))
f.write("%d %d %d %s\n"%(self.HARMONIC_FROM,self.HARMONIC_TO,self.HARMONIC_STEP,"Hmin Hmax Hstep"))
f.write("%d %d %d %d %s\n"%(self.HELICAL,self.METHOD,1,self.NEKS,"Helical Method Print_K Neks"))
f.write("foreground\n")
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),'tc.exe')
else:
command = "'" + os.path.join(locations.home_bin(), 'tc') + "'"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("Output file: %s"%("tc.out"))
print("\n--------------------------------------------------------\n")
#
# parse result files to exchange object
#
with open("tc.out","r") as f:
lines = f.readlines()
# print output file
# for line in lines:
# print(line, end="")
# remove returns
lines = [line[:-1] for line in lines]
harmonics_data = []
# separate numerical data from text
floatlist = []
harmoniclist = []
txtlist = []
for line in lines:
try:
tmp = line.strip()
if tmp.startswith("Harmonic"):
harmonic_number = int(tmp.split("Harmonic")[1].strip())
if harmonic_number != self.HARMONIC_FROM:
harmonics_data[-1][1] = harmoniclist
harmoniclist = []
harmonics_data.append([harmonic_number, None])
tmp = float(line.strip()[0])
floatlist.append(line)
harmoniclist.append(line)
except:
txtlist.append(line)
harmonics_data[-1][1] = harmoniclist
data = numpy.loadtxt(floatlist)
for index in range(0, len(harmonics_data)):
# print (harmonics_data[index][0], harmonics_data[index][1])
harmonics_data[index][1] = numpy.loadtxt(harmonics_data[index][1])
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", data)
calculated_data.add_content("xoppy_data_harmonics", harmonics_data)
calculated_data.add_content("plot_x_col", 1)
calculated_data.add_content("plot_y_col", 2)
except:
pass
try:
calculated_data.add_content("labels",["Energy (eV) without emittance", "Energy (eV) with emittance",
"Brilliance (ph/s/mrad^2/mm^2/0.1%bw)","Ky","Total Power (W)","Power density (W/mr^2)"])
except:
pass
try:
calculated_data.add_content("info",txtlist)
except:
pass
return calculated_data
def xoppy_calc_mlayer(self):
# copy the variable locally, so no more use of self.
MODE = self.MODE
SCAN = self.SCAN
F12_FLAG = self.F12_FLAG
SUBSTRATE = self.SUBSTRATE
ODD_MATERIAL = self.ODD_MATERIAL
EVEN_MATERIAL = self.EVEN_MATERIAL
ENERGY = self.ENERGY
THETA = self.THETA
SCAN_STEP = self.SCAN_STEP
NPOINTS = self.NPOINTS
ODD_THICKNESS = self.ODD_THICKNESS
EVEN_THICKNESS = self.EVEN_THICKNESS
NLAYERS = self.NLAYERS
FILE=self.FILE
for file in ["mlayer.inp","mlayer.par","mlayer.f12"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
#
# write input file for Fortran mlayer: mlayer.inp
#
f = open('mlayer.inp','w')
if SCAN == 0 and MODE == 0: a0 = 1
if SCAN == 1 and MODE == 0: a0 = 5
if SCAN == 0 and MODE == 1: a0 = 3
if SCAN == 1 and MODE == 1: a0 = 5
f.write("%d \n"%a0)
f.write("N\n")
f.write("%g\n"%( codata.h * codata.c / codata.e * 1e10 / ENERGY))
f.write("%g\n"%THETA)
if SCAN == 0:
f.write("%g\n"%SCAN_STEP)
a2 = codata.h * codata.c / codata.e * 1e10 / ENERGY
a3 = codata.h * codata.c / codata.e * 1e10 / (ENERGY + SCAN_STEP)
a4 = a3 - a2
if SCAN != 0:
f.write("%g\n"%a4)
f.write("%d\n"%NPOINTS)
if MODE == 0:
f.write("%d\n"%NLAYERS)
if MODE == 0:
if a0 != 5:
f.write("%g %g \n"%(ODD_THICKNESS,EVEN_THICKNESS))
else:
for i in range(NLAYERS):
f.write("%g %g \n"%(ODD_THICKNESS,EVEN_THICKNESS))
if MODE != 0:
f1 = open(FILE,'r')
a5 = f1.read()
f1.close()
if MODE != 0:
print("Number of layers in %s file is %d "%(FILE,NLAYERS))
f.write("%d\n"%NLAYERS)
f.write(a5)
f.write("mlayer.par\n")
f.write("mlayer.dat\n")
f.write("6\n")
f.close()
print('File written to disk: mlayer.inp')
#
# create f12 file
#
if F12_FLAG == 0:
energy = numpy.arange(0,500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
f12_s = f1f2_calc(SUBSTRATE,energy)
f12_e = f1f2_calc(EVEN_MATERIAL,energy)
f12_o = f1f2_calc(ODD_MATERIAL,energy)
f = open("mlayer.f12",'w')
f.write('; File created by xoppy for materials [substrate=%s,even=%s,odd=%s]: \n'%(SUBSTRATE,EVEN_MATERIAL,ODD_MATERIAL))
f.write('; Atomic masses: \n')
f.write("%g %g %g \n"%(xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(ODD_MATERIAL)) ))
f.write('; Densities: \n')
f.write("%g %g %g \n"%(xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(ODD_MATERIAL)) ))
f.write('; Number of energy points: \n')
f.write("%d\n"%(energy.size))
f.write('; For each energy point, energy[eV], f1[substrate], f2[substrate], f1[even], f2[even], f1[odd], f2[odd]: \n')
for i in range(energy.size):
f.write("%g %g %g %g %g %g %g \n"%(energy[i],f12_s[0,i],f12_s[1,i],f12_e[0,i],f12_e[1,i],f12_o[0,i],f12_o[1,i]))
f.close()
print('File written to disk: mlayer.f12')
#
# run external program mlayer
#
command = os.path.join(locations.home_bin(), 'mlayer') + " < mlayer.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("mlayer.dat"))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 3)
calculated_data.add_content("units_to_degrees", 1.0)
except:
pass
try:
calculated_data.add_content("labels",["Grazing angle Theta [deg]","s-reflectivity","p-reflectivity","averaged reflectivity","s-phase shift","p-phase shift","(s-electric field)^2","(p-electric field)^2"])
except:
pass
try:
info = "ML %s(%3.2f A):%s(%3.2f A) %d pairs; E=%5.3f eV"%(ODD_MATERIAL,ODD_THICKNESS,EVEN_MATERIAL,EVEN_THICKNESS,NLAYERS,ENERGY)
calculated_data.add_content("info",info)
except:
pass
return calculated_data