), "AZO5", 5.61)
zno = defineMat((
"O",
"Zn",
), (
0.1965,
0.8035,
), "ZnO", 5.61)
"""
coatedSubstrate(coating, thickness, substrate, det, e0=20.0,
withPoisson=True, nTraj=defaultNumTraj,
dose=defaultDose, sf=defaultCharFluor,
bf=defaultBremFluor, xtraParams=defaultXtraParams)
"""
spc_al = mc3.coatedSubstrate(ctg, c_thick, al, det, e0, True, n_traj, dose,
True, True, {})
sName = "%g nm C on Al at %g kV" % (1000 * c_thick, e0)
spc_al.rename(sName)
spc_al.display()
fi = wrkDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (n_traj)
spc_al.save(fi)
spc_azo2 = mc3.coatedSubstrate(ctg, c_thick, azo2, det, e0, True, n_traj, dose,
True, True, {})
sName = "%g nm C on AZO2 at %g kV" % (1000 * c_thick, e0)
spc_azo2.rename(sName)
spc_azo2.display()
fi = wrkDir + "/"
fi += sName
caf2 = material("CaF2", 3.18)
fe = material("Fe", 7.874)
si = material("Si", 2.329)
mgo = material("MgO", 3.58)
"""
coatedSubstrate(coating, thickness, substrate, det, e0=20.0,
withPoisson=True, nTraj=defaultNumTraj,
dose=defaultDose, sf=defaultCharFluor,
bf=defaultBremFluor, xtraParams=defaultXtraParams)
"""
spc_k411 = mc3.coatedSubstrate(ctg, c_thick, k411, det, e0, True, n_traj, dose,
True, True, {})
sName = "%g nm C on K411 at %g kV" % (1000 * c_thick, e0)
spc_k411.rename(sName)
spc_k411.display()
fi = wrkDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (n_traj)
spc_k411.save(fi)
spc_k412 = mc3.coatedSubstrate(ctg, c_thick, k412, det, e0, True, n_traj, dose,
True, True, {})
sName = "%g nm C on K412 at %g kV" % (1000 * c_thick, e0)
spc_k412.rename(sName)
spc_k412.display()
fi = wrkDir + "/"
fi += sName
homDir = homDir.replace('\\','/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/sim-nist-k961/"
e0 = 20.0
c_thick = 0.020 # 20 nm
n_traj = 10000
dose = 120.0
det = findDetector("Oxford p4 05eV 4K")
ctg = material("C", 1.8)
k961 = defineMat(( "O", "Na", "Mg", "Al", "Si", "P", "K" , "Ca", "Ti", "Mn", "Fe" ),
(0.470, 0.030, 0.030, 0.058, 0.299, 0.002, 0.025, 0.036, 0.012, 0.003, 0.035 ),
"K-961", 3.0)
# compute spectrum
spc_k961 = mc3.coatedSubstrate(ctg, c_thick, k961, det, e0, True, n_traj, dose, True, True, {})
spc_k961.rename("K-961")
spc_k961.setAsStandard(k961)
spc_k961.display()
sName = "20-nm-C-on-K961-glass-at-%g-kV" % (e0)
spc_k961.rename(sName)
spc_k961.display()
end = time.time()
delta = (end-start)/60
msg = "This script required %.3f min" % delta
print msg
if(delta > 60):
delta = delta/60
homDir = os.environ['HOME']
homDir = homDir.replace('\\','/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/utility"
outDir = homDir + "/Documents/git/dtsa2Scripts/utility/output/"
rptDir = wrkDir + '/test-mc3-simulate-coated-substrate Results/'
e0 = 20.0
det = findDetector("Probe")
mat = material("Fe2O3",5.0)
ctg = material("C", 1.8)
DataManager.clearSpectrumList()
spc = mc3.coatedSubstrate(ctg, 0.020, mat, det, 20.0,
True, 1000, 120.0, True,
True, {})
sName = "20 nm C on Fe2O3 at 20kV"
spc.rename(sName)
spc.display()
shutil.rmtree(rptDir)
print "Done!"
end = time.time()
delta = (end-start)/60
msg = "This script required %.3f min" % delta
print msg
if(delta > 60):
delta = delta/60
msg = "...or %.3f hr" % delta
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
stds = {
element("O"): spc_zno_std,
element("Zn"): spc_zno_std,
element("Si"): spc_si_std
}
print(
"Specimen Name \t\t Oxygen Ka1 K-Ratio \t Zinc La1 K-Ratio \t Si Ka K-Ratio "
)
#5 nm ZnO on Si at 4 kV 0.073166 ± 0.000133 0.075862 ± 0.000106 0.877289 ± 0.000202
for thNm in lThNm:
thUm = thNm / 1000.
spc = mc3.coatedSubstrate(zno, thUm, si, det, e0, True, nTraj, dose, True,
True, xtraParams)
sName = "%g nm ZnO on Si at %g kV" % (thNm, e0)
spc.rename(sName)
spc.display()
fi = resDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
ff = epq.FilterFit(det, epq.ToSI.keV(e0))
ff.addReference(element("O"), spc_zno_std)
ff.addReference(element("Zn"), spc_zno_std)
ff.addReference(element("Si"), spc_si_std)
kr = ff.getKRatios(spc)
kO = kr.getKRatioU(
epq.XRayTransition(epq.Element.O, epq.XRayTransition.KA1))
lab6 = defineMat((
"La",
"B",
), (
0.68168,
0.31832,
), "LaB6", 4.72)
lapo4 = defineMat(("La", "P", "O"), (
0.59393,
0.13243,
0.27364,
), "LaPO4", 4.93)
# compute spectrum
spc_lab6 = mc3.coatedSubstrate(ctg, c_thick, lab6, det, e0, True, n_traj, dose,
True, True, {})
spc_lab6.rename("LaB6")
# spc_lab6.setAsStandard(lab6)
spc_lab6.display()
sName = "20-nm-C-on-LaB6-%g-kV" % (e0)
spc_lab6.rename(sName)
spc_lab6.display()
end = time.time()
delta = (end - start) / 60
msg = "This script required %.3f min" % delta
print msg
if (delta > 60):
delta = delta / 60
msg = "...or %.3f hr" % delta
ELEM: O MgO Al2O3 SiO2 CaO FeO
XRAY: ka ka ka ka ka ka
OXWT: .000 .191 .096 .460 .149 .103
ELWT: .432 .115 .051 .215 .107 .080
KFAC: .0017 .0008 .0003 .0016 .0010 .0007
ZCOR: 2.5028 1.4996 1.4628 1.3079 1.0816 1.1834
AT% : 59.477 10.446 4.166 16.879 5.873 3.161
24 O: 24.000 4.215 1.681 6.811 2.370 1.276
"""
# simulate K412-NR
spc_k412nr = mc3.coatedSubstrate(ctg, c_thick, k412nr, det, e0, True, n_traj,
dose, True, True, {})
sName = "%g nm C on K412-NR at %g kV" % (1000 * c_thick, e0)
spc_k412nr.rename(sName)
spc_k412nr.display()
fi = wrkDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (n_traj)
spc_k412nr.setAsStandard(k412nr)
spc_k412nr.save(fi)
# simulate K412-JF
spc_k412jf = mc3.coatedSubstrate(ctg, c_thick, k412jf, det, e0, True, n_traj,
dose, True, True, {})
sName = "%g nm C on K412-JF at %g kV" % (1000 * c_thick, e0)
spc_k412jf.rename(sName)
spc_k412jf.setAsStandard(k412jf)
ni2p = material("Ni2P", 7.39)
fe = material("Fe", 7.874)
s310 = defineMat(("P", "S", "Cr", "Mn", "Fe", "Ni", ),
(0.0004,0.0003,0.2500,0.0200,0.5069,0.2050),
"S310", 7.89)
srm1155 = defineMat(("C" , "Co", "Cr", "Cu", "Mn" , "Mo", "Ni", "S", "V",),
(0.0445, 0.1052, 18.37, 0.1734, 1.619, 2.386, 12.35, 0.0175, 0.0508),
"SRM-1155", 7.89)
# Fe
spc_fe = mc3.coatedSubstrate(ctg, c_thick, fe, det, e0,
True, n_traj, dose, True, True, {})
sName = "%g nm C on Fe at %g kV" % (1000*c_thick, e0)
spc_fe.rename(sName)
spc_fe.display()
fi = wrkDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (n_traj)
spc_fe.setAsStandard(fe)
spc_fe.save(fi)
# S310
spc_s310 = mc3.coatedSubstrate(ctg, c_thick, s310, det, e0,
True, n_traj, dose, True, True, {})
sName = "%g nm C on S310 at %g kV" % (1000*c_thick, e0)
spc_s310.rename(sName)
spc_s310.setAsStandard(s310)
trs = mc3.suggestTransitions(si, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
stds = { element("O"): spc_zno_std, element("Zn"): spc_zno_std, element("Si"): spc_si_std }
print("Specimen Name \t\t Oxygen Ka1 K-Ratio \t Zinc La1 K-Ratio \t Si Ka K-Ratio ")
#5 nm ZnO on Si at 4 kV 0.073166 ± 0.000133 0.075862 ± 0.000106 0.877289 ± 0.000202
for thNm in lThNm:
thUm = thNm/1000.
spc = mc3.coatedSubstrate(zno, thUm, si, det, e0,
True, nTraj, dose, True,
True, xtraParams)
sName = "%g nm ZnO on Si at %g kV" % (thNm, e0)
spc.rename(sName)
spc.display()
fi = resDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
ff=epq.FilterFit(det,epq.ToSI.keV(e0))
ff.addReference(element("O"), spc_zno_std)
ff.addReference(element("Zn"), spc_zno_std)
ff.addReference(element("Si"), spc_si_std)
kr = ff.getKRatios(spc)
kO = kr.getKRatioU(epq.XRayTransition(epq.Element.O, epq.XRayTransition.KA1))
for dir in dirs:
dir = dir.replace('\\', '/')
print(dir)
shutil.rmtree(dir)
iCount += 1
lThickC = range( tNmStepC, tNmMaxC+tNmStepC, tNmStepC)
for tNmC in lThickC:
ts = time.time()
spc = mc3.coatedSubstrate(c, tNmC*1.0e-3, si, det, e0, True,
nTraj, dose, True, True, xp)
spc = epq.SpectrumUtils.addNoiseToSpectrum(spc, 1.0)
spc = wrap(spc)
sName = "%g-nm-C-on-Si-%g-kV-%d-traj" % (tNmC, e0, nTraj)
spc.rename(sName)
res = anaConSi(spc, det, digits=2, display=False)
cI = res["C"]
siI = res["Si"]
lT.append(tNmC)
lPICmu.append(cI[0])
lPICuc.append(cI[1])
lPISimu.append(siI[0])
lPISiuc.append(siI[1])
iCount += 1
te = time.time()
d = (te-ts) / 60.0
homDir = homDir.replace('\\', '/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/sim-nist-k1526/"
e0 = 20.0
c_thick = 0.020 # 20 nm
n_traj = 10000
dose = 120.0
det = findDetector("Oxford p4 05eV 4K")
ctg = material("C", 1.8)
k1526 = defineMat(
("Li", "F", "Na", "Al", "P", "Br", "O"),
(0.03908, 0.20274, 0.05475, 0.06135, 0.211245, 0.06441, 0.237405),
"K-15275", 3.30)
# compute spectrum
spc_k1526 = mc3.coatedSubstrate(ctg, c_thick, k1526, det, e0, True, n_traj,
dose, True, True, {})
spc_k1526.rename("K-1526")
spc_k1526.setAsStandard(k1526)
spc_k1526.display()
sName = "20-nm-C-on-K1526-glass-at-%g-kV" % (e0)
spc_k1526.rename(sName)
spc_k1526.display()
end = time.time()
delta = (end - start) / 60
msg = "This script required %.3f min" % delta
print msg
if (delta > 60):
delta = delta / 60
ctg = material("C", 1.8)
mno2 = material("MnO2", 5.03)
mn = material("Mn", 7.42)
sio2 = material("SiO2", 2.65)
"""
coatedSubstrate(coating, thickness, substrate, det, e0=20.0,
withPoisson=True, nTraj=defaultNumTraj,
dose=defaultDose, sf=defaultCharFluor,
bf=defaultBremFluor, xtraParams=defaultXtraParams)
"""
spc_mno2 = mc3.coatedSubstrate(ctg, c_thick, mno2, det, e0, True, n_traj, dose,
True, True, {})
sName = "%g-nm-C-on-MnO2-at-%g-kV" % (1000 * c_thick, e0)
spc_mno2.rename(sName)
spc_mno2.display()
fi = wrkDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (n_traj)
spc_mno2.setAsStandard(mno2)
print(fi)
spc_mno2.save(fi)
spc_sio2 = mc3.coatedSubstrate(ctg, c_thick, sio2, det, e0, True, n_traj, dose,
True, True, {})
sName = "%g-nm-C-on-SiO2-at-%g-kV" % (1000 * c_thick, e0)
spc_sio2.rename(sName)
spc_sio2.display()
e0 = 20.0
c_thick = 0.020 # 20 nm
n_traj = 10000
dose = 120.0
det = findDetector("Oxford p4 05eV 4K")
ctg = material("C", 1.8)
pyrex = defineMat(( "B", "O", "Na", "Mg", "Al", "Si",
"Cl", "Ca", "Fe" ),
(0.0392, 0.5384, 0.0312, 0.0003, 0.0117, 0.3772,
0.0010, 0.0007, 0.0003),
"pyrex", 2.5)
# compute spectrum
spc_pyrex = mc3.coatedSubstrate(ctg, c_thick, pyrex, det, e0, True,
n_traj, dose, True, True, {})
spc_pyrex.rename("pyrex")
spc_pyrex.setAsStandard(pyrex)
spc_pyrex.display()
sName = "20-nm-C-on-Pyrex-at-%g-kV" % (e0)
spc_pyrex.rename(sName)
spc_pyrex.display()
end = time.time()
delta = (end-start)/60
msg = "This script required %.3f min" % delta
print msg
if(delta > 60):
delta = delta/60
path = outDir + "/*/"
# clean up any un-needed MC* output directories
dirs = glob.glob(path)
for dir in dirs:
dir = dir.replace('\\', '/')
print(dir)
shutil.rmtree(dir)
iCount += 1
lThickC = range(tNmStepC, tNmMaxC + tNmStepC, tNmStepC)
for tNmC in lThickC:
ts = time.time()
spc = mc3.coatedSubstrate(c, tNmC * 1.0e-3, si, det, e0, True, nTraj, dose,
True, True, xp)
spc = epq.SpectrumUtils.addNoiseToSpectrum(spc, 1.0)
spc = wrap(spc)
sName = "%g-nm-C-on-Si-%g-kV-%d-traj" % (tNmC, e0, nTraj)
spc.rename(sName)
res = anaConSi(spc, det, digits=2, display=False)
cI = res["C"]
siI = res["Si"]
lT.append(tNmC)
lPICmu.append(cI[0])
lPICuc.append(cI[1])
lPISimu.append(siI[0])
lPISiuc.append(siI[1])
iCount += 1
te = time.time()
d = (te - ts) / 60.0
homDir = homDir.replace('\\', '/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/simulateCorning1737Glass/"
ctg = material("C", 1.8)
c1737 = defineMat(("Ba", "Sr", "As", "Ca", "Si", "Al", "Mg", "O", "B"),
(0.0863, 0.1502, 0.0428, 0.02862, 0.27676, 0.08863, 0.00486,
0.47299, 0.02254), "Corning 1737 Glass", 2.540)
"""
coatedSubstrate(coating, thickness, substrate, det, e0=20.0,
withPoisson=True, nTraj=defaultNumTraj,
dose=defaultDose, sf=defaultCharFluor,
bf=defaultBremFluor, xtraParams=defaultXtraParams)
"""
spc_c1737 = mc3.coatedSubstrate(ctg, c_thick, c1737, det, e0, True, n_traj,
dose, True, True, {})
sName = "%g nm C on Corning 1737 Glass at %g kV" % (1000 * c_thick, e0)
spc_c1737.rename(sName)
spc_c1737.display()
spc_c1737.setAsStandard(c1737)
fi = wrkDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (n_traj)
spc_c1737.save(fi)
end = time.time()
delta = (end - start) / 60
msg = "This script required %.3f min" % delta
print msg
if (delta > 60):
delta = delta / 60
b = material("B", density=2.37)
bn = material("BN", density=2.1)
aln = material("AlN", density=3.26)
"""
Simulate a spectrum of a coating on a substrate.
Monte Carlo simulate a spectrum from a 'substrate' material coated
with 'coating' of the specified thickness (in microns).
coatedSubstrate(coating, thickness, substrate, det, e0=20.0,
withPoisson=True, nTraj=defaultNumTraj,
dose=defaultDose, sf=defaultCharFluor,
bf=defaultBremFluor, xtraParams=defaultXtraParams)
"""
spc_bn = mc.coatedSubstrate(c, 20.0e-03, bn, det, 5.0, True, nTraj, dose, True,
True, {})
spc_bn.rename("10-nm-C-on-BN-5-kV")
spc_bn.setAsStandard(bn)
spc_bn.display()
spc_b = mc.coatedSubstrate(c, 20.0e-03, b, det, 5.0, True, nTraj, dose, True,
True, {})
spc_b.rename("10-nm-C-on-B-5-kV")
spc_b.setAsStandard(b)
spc_b.display()
spc_aln = mc.coatedSubstrate(c, 20.0e-03, aln, det, 5.0, True, nTraj, dose,
True, True, {})
spc_aln.rename("10-nm-C-on-AlN-5-kV")
spc_aln.setAsStandard(aln)
spc_aln.display()