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_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
class OWxpowder_fml(XoppyWidget):
name = "POWDER_FML"
id = "orange.widgets.dataxpowder_fml"
description = "X-ray Powder Diffraction Pattern"
icon = "icons/xoppy_xpowder_fml.png"
priority = 23
category = ""
keywords = ["xoppy", "xpowder_fml"]
FILE = Setting(
os.path.join(
locations.home_data(),
"cif" + os.sep + "icsd_31142_sepiolite_BraunerPreisinger.cif"))
TITLE = Setting("powder pattern using crysFML")
LAMBDA = Setting(1.54056)
JOB = Setting(0)
U = Setting(0.0002)
V = Setting(-0.0002)
W = Setting(0.012)
X = Setting(0.0019)
LS = Setting(1900.0)
THMIN = Setting(1.0)
STEP = Setting(0.05)
THMAX = Setting(135.0)
def build_gui(self):
box = oasysgui.widgetBox(self.controlArea,
self.name + " Input Parameters",
orientation="vertical",
width=self.CONTROL_AREA_WIDTH - 5)
idx = -1
#widget index 0
idx += 1
box1 = gui.widgetBox(box)
file_box = oasysgui.widgetBox(box1,
"",
addSpace=False,
orientation="horizontal",
height=25)
self.le_file = oasysgui.lineEdit(file_box,
self,
"FILE",
label=self.unitLabels()[idx],
addSpace=False,
orientation="horizontal")
self.show_at(self.unitFlags()[idx], box1)
gui.button(file_box, self, "...", callback=self.selectFile)
#widget index 1
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"TITLE",
label=self.unitLabels()[idx],
addSpace=False,
orientation="horizontal")
self.show_at(self.unitFlags()[idx], box1)
#widget index 2
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"LAMBDA",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 3
idx += 1
box1 = gui.widgetBox(box)
gui.comboBox(box1,
self,
"JOB",
label=self.unitLabels()[idx],
addSpace=False,
items=['X rays', 'Neutrons'],
valueType=int,
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 4
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"U",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 5
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"V",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 6
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"W",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 7
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"X",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 8
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"LS",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 9
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"THMIN",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 10
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"STEP",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
#widget index 11
idx += 1
box1 = gui.widgetBox(box)
oasysgui.lineEdit(box1,
self,
"THMAX",
label=self.unitLabels()[idx],
addSpace=False,
valueType=float,
validator=QDoubleValidator(),
orientation="horizontal",
labelWidth=250)
self.show_at(self.unitFlags()[idx], box1)
def unitLabels(self):
return [
'CIF File: ', 'Title:', 'Lambda [A]: ', 'Radiation:', 'U: ', 'V: ',
'W: ', 'X: ', 'Ls:', 'TwoTheta from [deg]', 'TwoTheta step: ',
'TwoTheta to', 'None'
]
def unitFlags(self):
return [
'1', '1', '1', '1', '1', '1', '1', '1', '1', '1', '1', '1', '1'
]
def selectFile(self):
self.le_file.setText(
oasysgui.selectFileFromDialog(self,
self.FILE,
"Open CIF File",
file_extension_filter="*.cif"))
def get_help_name(self):
return 'powder_fml'
def check_fields(self):
congruence.checkFile(self.FILE)
self.LAMBDA = congruence.checkStrictlyPositiveNumber(
self.LAMBDA, "Lambda")
self.U = congruence.checkNumber(self.U, "U")
self.V = congruence.checkNumber(self.V, "V")
self.W = congruence.checkNumber(self.W, "W")
self.X = congruence.checkNumber(self.X, "X")
self.LS = congruence.checkNumber(self.LS, "LS")
self.THMIN = congruence.checkPositiveAngle(self.THMIN, "TwoTheta from")
self.THMAX = congruence.checkPositiveAngle(self.THMAX, "TwoTheta to")
self.STEP = congruence.checkStrictlyPositiveAngle(
self.STEP, "TwoTheta step")
congruence.checkGreaterThan(self.THMAX, self.THMIN, "TwoTheta to",
"TwoTheta from")
def do_xoppy_calculation(self):
return self.xoppy_calc_xpowder_fml()
def extract_data_from_xoppy_output(self, calculation_output):
return calculation_output
def get_data_exchange_widget_name(self):
return "XPOWDER_FML"
def getTitles(self):
return ["Diffraction Pattern"]
def getXTitles(self):
return ["TwoTheta[Deg]"]
def getYTitles(self):
return ["Intensity[a.u.]"]
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))
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_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
