def anaMcNiCuKa(spc, det, stdBase, maxCh=1200):
props=spc.getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
lt = props.getNumericProperty(epq.SpectrumProperties.LiveTime)
pc = props.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
wkDst = props.getNumericProperty(epq.SpectrumProperties.WorkingDistance)
spc = jmg.cropSpec(spc, end=maxCh)
unSpc = jmg.updateCommonSpecProps(spc, det, liveTime=lt, probeCur=pc, e0=e0, wrkDist=wkDst)
dt2.display(unSpc)
# define the transitions I want to measure
tsNiKa = epq.XRayTransitionSet(epq.Element.Ni, epq.XRayTransitionSet.K_FAMILY)
tsCuKa = epq.XRayTransitionSet(epq.Element.Cu, epq.XRayTransitionSet.K_FAMILY)
trs = [tsNiKa, tsCuKa]
relStd = "/%gkV/" % (e0)
stdDir = stdBase + relStd
niFile = stdDir + "Ni-sim.msa"
cuFile = stdDir + "Cu-sim.msa"
spc = dt2.wrap(ept.SpectrumFile.open(niFile)[0])
props=spc.getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
lt = props.getNumericProperty(epq.SpectrumProperties.LiveTime)
pc = props.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
wkDst = props.getNumericWithDefault(epq.SpectrumProperties.WorkingDistance, wkDst)
spc = jmg.cropSpec(spc, end=maxCh)
niSpc = jmg.updateCommonSpecProps(spc, det, liveTime=lt, probeCur=pc, e0=e0, wrkDist=wkDst)
dt2.display(niSpc)
spc = dt2.wrap(ept.SpectrumFile.open(cuFile)[0])
props=spc.getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
lt = props.getNumericProperty(epq.SpectrumProperties.LiveTime)
pc = props.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
wkDst = props.getNumericWithDefault(epq.SpectrumProperties.WorkingDistance, wkDst)
spc = jmg.cropSpec(spc, end=maxCh)
cuSpc = jmg.updateCommonSpecProps(spc, det, liveTime=lt, probeCur=pc, e0=e0, wrkDist=wkDst)
dt2.display(cuSpc)
niStd = {"El":dt2.element("Ni"), "Spc":niSpc}
cuStd = {"El":dt2.element("Cu"), "Spc":cuSpc}
stds = [niStd, cuStd]
theKR = jmg.compKRs(unSpc, stds, trs, det, e0)
krNiCalc = theKR[0]
krCuCalc = theKR[1]
return [krNiCalc, krCuCalc]
lNm=[]
lKCK=[]
lKCuL=[]
for i in range(500):
tNmC = float(i+1)
lNm.append(tNmC)
sLay = [[c, tNmC/1.0e9], [cu, 100.0]]
sSpc = mc3.multiFilm(sLay, det, e0=e0, withPoisson=True, nTraj=nTraj, dose=dose, sf=charF, bf=bremF, xtraParams={})
sp=sSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName,"%g-nm-C-on-Cu"% tNmC)
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, dose)
sp.setNumericProperty(epq.SpectrumProperties.FaradayEnd, dose)
# display(sSpc)
a = jmg.compKRs(sSpc, stds, trs, det, e0)
lKCK.append(a[0])
lKCuL.append(a[1])
print (i+1)
# prepare the output file
csvPath = csvDir + "/sim-C-on-Cu-%gkV.csv" % e0
f=open(csvPath, 'w')
strLine = 'tNm, kCKa, kCuLa\n'
f.write(strLine)
l = len(lNm)
for i in range(l):
strLine = '%.1f, %.5f, %.5f\n' % (lNm[i], lKCK[i], lKCuL[i])
f.write(strLine)
f.close()
def simLineInMatrix(lin,
linMat,
blk,
blkMat,
nmLinWid,
umBlock,
nPts,
trs,
outDir,
hdr,
det,
e0,
lt,
pc,
withPoisson=True,
nTraj=100,
sf=True,
bf=True,
iDigits=5,
bVerbose=False,
xtraParams={}):
"""simLineInMatrix(lin, linMat, blk, blkMat, nmLinWid, umBlock, nPts,
trs, outDir, hdr, det, e0, lt, pc, withPoisson=True, nTraj=nTraj,
sf=True, bf=True, iDigits=5, bVerbose=False, xtraParams={})
Simulate a line of width `nmLinWid' nm at the center of a block of
`umBlock' microns. The line is of material `lin' with a name `linMat'.
The block is of material `blk' with a name `blkMat'.
We analyze an list `trs' of transitions, writing the K-ratios to a
.csv file with a header `hdr'. We use the detector `det', voltage `e0'
(kV) and live time `lt' sec and probe current `pc' nA. This will
compute the standard spectra, compute the spectra for nPts+1 from
-nPts/2 ... 0 ...nPts/2 times the block size. It will then compute the
K-ratios for each spectrum and write them to a file `name' in outDir
with a header `hdr' that matches the transition order.
"""
# order is order of trs..
sc = 1.0e-6 # scale from microns to meters for positions
lX = [] # an array for postions
lKlin = [] # an array for the K-ratio of the line
lKblk = [
] # an array for the K-ratio of the block. Title correspond to hdr string
# start clean
dt2.DataManager.clearSpectrumList()
# create the standards
linStd = simulateBulkStandard(lin,
linMat,
det,
e0,
lt,
pc,
withPoisson=True,
nTraj=nTraj,
sf=True,
bf=True,
xtraParams={})
dt2.display(linStd)
blkStd = simulateBulkStandard(blk,
blkMat,
det,
e0,
lt,
pc,
withPoisson=True,
nTraj=nTraj,
sf=True,
bf=True,
xtraParams={})
dt2.display(blkStd)
lStd = {"El": dt2.element(linMat), "Spc": linStd}
bStd = {"El": dt2.element(blkMat), "Spc": blkStd}
stds = [lStd, bStd] # note: put the transitions in this order
iCount = 0
for x in range(-nPts / 2, (nPts / 2) + 1, 1):
xv = sc * x * umBlock / nPts
lX.append(round(x * umBlock / nPts, iDigits))
monte = nm.MonteCarloSS()
monte.setBeamEnergy(epq.ToSI.keV(e0))
# use a 1 nm probe
beam = nm.GaussianBeam(1.0e-9)
monte.setElectronGun(beam)
beam.setCenter([xv, 0.0, -0.05])
# createBlock(double[] dims, double[] point, double phi, double theta, double psi)
# createBlock - Create a block of:
# dimensions specified in dims,
# centered at point,
# then rotated by the euler angles phi, theta, psi.
block = nm.MultiPlaneShape.createBlock(
[umBlock * 1.0e-6, umBlock * 1.0e-6, umBlock * 1.0e-6],
[0.0, 0.0, 0.5 * umBlock * 1.0e-6], 0.0, 0.0, 0.0)
matrix = monte.addSubRegion(monte.getChamber(), blk, block)
monte.addSubRegion(
matrix, lin,
nm.MultiPlaneShape.createBlock(
[1.0e-9 * nmLinWid, umBlock * 1.0e-6, umBlock * 1.0e-6],
[0.0, 0.0, 0.5 * umBlock * 1.0e-6], 0.0, 0.0, 0.0))
det.reset()
# Add event listeners to model characteristic radiation
chXR = nm3.CharacteristicXRayGeneration3.create(monte)
xrel = nm3.XRayTransport3.create(monte, det, chXR)
brXR = nm3.BremsstrahlungXRayGeneration3.create(monte)
brem = nm3.XRayTransport3.create(monte, det, brXR)
fxg3 = nm3.FluorescenceXRayGeneration3.create(monte, chXR)
chSF = nm3.XRayTransport3.create(monte, det, fxg3)
brSF = nm3.XRayTransport3.create(
monte, det, nm3.FluorescenceXRayGeneration3.create(monte, brXR))
# here is where we run the simulation
monte.runMultipleTrajectories(nTraj)
spec = det.getSpectrum((lt * pc * 1.0e-9) /
(nTraj * epq.PhysicalConstants.ElectronCharge))
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.FaradayEnd, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
spcName = "x = %.3f um" % x
epq.SpectrumUtils.rename(spec, spcName)
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
# display(spec)
a = jmg.compKRs(spec, stds, trs, det, e0)
iCount += 1
print(iCount)
lKlin.append(round(a[0], iDigits))
lKblk.append(round(a[1], iDigits))
basFile = "%gnm-%s-in-%gum-%s-%gkV-%g-Traj.csv" % (
nmLinWid, linMat, umBlock, blkMat, e0, nTraj)
strOutFile = outDir + "/" + basFile
f = open(strOutFile, 'w')
strLine = hdr + '\n'
f.write(strLine)
for i in range(iCount):
strLine = "%.5f" % lX[i] + ","
strLine = strLine + "%.5f" % lKlin[i] + ","
strLine = strLine + "%.5f" % lKblk[i] + "\n"
f.write(strLine)
f.close()
def simLineInMatrixLimScan(lin,
linMat,
blk,
blkMat,
nmLinWid,
umBlock,
nmScan,
nPts,
trs,
outDir,
hdr,
det,
e0,
lt,
pc,
withPoisson=True,
nTraj=100,
sf=True,
bf=True,
iDigits=5,
bVerbose=False,
xtraParams={}):
"""simLineInMatrixLimScan(lin, linMat, blk, blkMat, nmLinWid, umBlock,
nmScan, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True,
nTraj=nTraj, sf=True, bf=True, iDigits=5, bVerbose=False,
xtraParams={})
Simulate a line of width `nmLinWid' nm at the center of a block of
`umBlock' microns. The line is of material `lin' with a name `linMat'.
The block is of material `blk' with a name `blkMat'. We step a total
distance of nmScan across the center of the line.
We analyze an list `trs' of transitions, writing the K-ratios to a
.csv file with a header `hdr'. We use the detector `det', voltage `e0'
(kV) and live time `lt' sec and probe current `pc' nA. This will
compute the standard spectra, compute the spectra the scanned
region. It will then compute the K-ratios for each spectrum and write
them to a file `name' in outDir with a header `hdr' that matches the
transition order.
"""
# order is order of trs..
sc = 1.0e-6 # scale from microns to meters for positions
dose = lt * pc
lX = [] # an array for postions
lKlin = [] # an array for the K-ratio of the line
lKblk = [
] # an array for the K-ratio of the block. Title correspond to hdr string
umLine = nmLinWid * 1.0e-3
# start clean
dt2.DataManager.clearSpectrumList()
# create the standards
linStd = simulateBulkStandard(lin,
linMat,
det,
e0,
lt,
pc,
withPoisson=withPoisson,
nTraj=nTraj,
sf=sf,
bf=bf,
xtraParams={})
dt2.display(linStd)
blkStd = simulateBulkStandard(blk,
blkMat,
det,
e0,
lt,
pc,
withPoisson=withPoisson,
nTraj=nTraj,
sf=sf,
bf=sf,
xtraParams={})
dt2.display(blkStd)
lStd = {"El": dt2.element(linMat), "Spc": linStd}
bStd = {"El": dt2.element(blkMat), "Spc": blkStd}
stds = [lStd, bStd] # note: put the transitions in this order
iCount = 0
for x in range(-nPts / 2, (nPts / 2) + 1, 1):
xPosNm = x * nmScan / nPts
lX.append(round(xPosNm, iDigits))
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(trs,
charAccum=sf,
charFluorAccum=sf,
bremFluorAccum=bf))
xtraParams.update(mc3.configureOutput(outDir))
xtraParams.update(mc3.configureBeam(xPosNm * 1.0e-09, 0, -0.099, 1.0))
spec = mc3.embeddedRectangle(lin,
[umLine * sc, umBlock * sc, umBlock * sc],
blk,
0,
det,
e0,
withPoisson=withPoisson,
nTraj=nTraj,
dose=dose,
sf=sf,
bf=bf,
xtraParams=xtraParams)
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.FaradayEnd, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
spcName = "x = %.3f um" % x
epq.SpectrumUtils.rename(spec, spcName)
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
# display(spec)
a = jmg.compKRs(spec, stds, trs, det, e0)
iCount += 1
print(iCount, xPosNm)
lKlin.append(round(a[0], iDigits))
lKblk.append(round(a[1], iDigits))
basFile = "%gnm-%s-in-%gum-%s-%gkV-%g-Traj.csv" % (
nmLinWid, linMat, umBlock, blkMat, e0, nTraj)
strOutFile = outDir + "/" + basFile
f = open(strOutFile, 'w')
strLine = hdr + '\n'
f.write(strLine)
for i in range(iCount):
strLine = "%.3f" % lX[i] + ","
strLine = strLine + "%.5f" % lKlin[i] + ","
strLine = strLine + "%.5f" % lKblk[i] + "\n"
f.write(strLine)
f.close()
det,
e0=e0,
withPoisson=True,
nTraj=nTraj,
dose=dose,
sf=charF,
bf=bremF,
xtraParams={})
sp = sSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName,
"%g-nm-Au-on-Cu" % tNmAu)
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, dose)
sp.setNumericProperty(epq.SpectrumProperties.FaradayEnd, dose)
display(sSpc)
a = jmg.compKRs(sSpc, stds, trs, det, e0)
print(a[0])
print(a[1])
lKAuL.append(a[0])
lKCuK.append(a[1])
print(i + 1)
# prepare the output file
csvPath = csvDir + "/sim-Au-on-Cu-%g-kV-%g-steps-%g-nm.csv" % (e0, nSteps,
tNmStep)
f = open(csvPath, 'w')
strLine = 'tNm, kAuLaMu, kAuLaStd, kCuKaMu, kCuKaStd\n'
f.write(strLine)
l = len(lNm)
for i in range(l):
strLine = '%.1f, %.5f, %.5f, %.5f, %.5f\n' % (
msg = "Simulating %g nm C on Fe at %g kV %g traj" % (tc, e0, nTraj)
print(msg)
spc = sim_amc_coated_mat(fe, det, e0, nTraj, lt=lt, pc=pc, tc=tc)
display(spc)
sName = "%g-nm-C-on-Fe-%g-kV-%g-traj" % (tc, e0, nTraj)
fi = datDir + "/"
fi += sName
fi += ".msa"
if bSaveSpc == True:
spc.save(fi)
endCycle = time.time()
delta = (endCycle-startCycle)/60
tod = datetime.datetime.now().time()
msg = "C layer %g of %g required %.3f min %s" % (i, nSpec, delta, tod)
print msg
res = jmg.compKRs(spc, stds, trs, det, e0)
print(res)
lNmC.append(tc)
lkC.append(round(res[0], 5))
lkFe.append(round(res[1], 5))
nMeas = len(lkFe)
f = open(csvFil, 'w')
strLine = 't.nm, kC, kFe\n'
f.write(strLine)
for i in range(nMeas):
strLine = "%g" % lNmC[i] + ","
strLine = strLine + "%.5f" % lkC[i] + ","
strLine = strLine + "%.5f" % lkFe[i] + "\n"
f.write(strLine)
f.close()
l_nm_C = []
l_kC_mu = []
l_kC_unc = []
l_kFe_mu = []
l_kFe_unc = []
for tc in lNmCsim:
sName = "%g-nm-C-on-Fe-%g-kV-%g-traj" % (tc, e0, nTraj)
fi = datDir + "/"
fi += sName
fi += ".msa"
# print(fi)
spc = readSpectrum(fi)
display(spc)
kr = jmg.compKRs(spc, stds, trs, det, e0, digits=5)
l_nm_C.append(tc)
l_kC_mu.append(kr[0][0])
l_kC_unc.append(kr[0][1])
l_kFe_mu.append(kr[1][0])
l_kFe_unc.append(kr[1][1])
# print(kr)
f=open(csvFil, 'w')
strLine = 'nm_c,c_ka_mu,c_ka_unc,fe_la_mu,fe_la_unc\n'
f.write(strLine)
for i in range(nSpec):
strLine = "%g" % l_nm_C[i] + ","
strLine = strLine + "%.5f" % l_kC_mu[i] + ","
strLine = strLine + "%.5f" % l_kC_unc[i] + ","
strLine = strLine + "%.5f" % l_kFe_mu[i] + ","
def simLineInMatrixLimScan(lin, linMat, blk, blkMat, nmLinWid, umBlock,nmScan, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True, nTraj=100, sf=True, bf=True, iDigits=5, bVerbose=False, xtraParams={}):
"""simLineInMatrixLimScan(lin, linMat, blk, blkMat, nmLinWid, umBlock,
nmScan, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True,
nTraj=nTraj, sf=True, bf=True, iDigits=5, bVerbose=False,
xtraParams={})
Simulate a line of width `nmLinWid' nm at the center of a block of
`umBlock' microns. The line is of material `lin' with a name `linMat'.
The block is of material `blk' with a name `blkMat'. We step a total
distance of nmScan across the center of the line.
We analyze an list `trs' of transitions, writing the K-ratios to a
.csv file with a header `hdr'. We use the detector `det', voltage `e0'
(kV) and live time `lt' sec and probe current `pc' nA. This will
compute the standard spectra, compute the spectra the scanned
region. It will then compute the K-ratios for each spectrum and write
them to a file `name' in outDir with a header `hdr' that matches the
transition order.
"""
# order is order of trs..
sc = 1.0e-6 # scale from microns to meters for positions
dose = lt*pc
lX = [] # an array for postions
lKlin = [] # an array for the K-ratio of the line
lKblk = [] # an array for the K-ratio of the block. Title correspond to hdr string
umLine = nmLinWid * 1.0e-3
# start clean
dt2.DataManager.clearSpectrumList()
# create the standards
linStd = simulateBulkStandard(lin, linMat, det, e0, lt, pc, withPoisson=withPoisson, nTraj=nTraj, sf=sf, bf=bf, xtraParams={})
dt2.display(linStd)
blkStd = simulateBulkStandard(blk, blkMat, det, e0, lt, pc, withPoisson=withPoisson, nTraj=nTraj, sf=sf, bf=sf, xtraParams={})
dt2.display(blkStd)
lStd = {"El":dt2.element(linMat), "Spc":linStd}
bStd = {"El":dt2.element(blkMat), "Spc":blkStd}
stds = [lStd, bStd] # note: put the transitions in this order
iCount = 0
for x in range(-nPts/2, (nPts/2)+1, 1):
xPosNm = x * nmScan / nPts
lX.append(round(xPosNm, iDigits))
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(trs, charAccum=sf, charFluorAccum=sf, bremFluorAccum=bf))
xtraParams.update(mc3.configureOutput(outDir))
xtraParams.update(mc3.configureBeam(xPosNm*1.0e-09, 0, -0.099, 1.0))
spec = mc3.embeddedRectangle(lin, [umLine*sc, umBlock*sc, umBlock*sc], blk, 0, det, e0, withPoisson=withPoisson, nTraj=nTraj, dose=dose, sf=sf, bf=bf, xtraParams=xtraParams)
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.FaradayEnd, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
spcName = "x = %.3f um" % x
epq.SpectrumUtils.rename(spec, spcName)
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
# display(spec)
a = jmg.compKRs(spec, stds, trs, det, e0)
iCount += 1
print(iCount, xPosNm)
lKlin.append(round(a[0], iDigits))
lKblk.append(round(a[1], iDigits))
basFile ="%gnm-%s-in-%gum-%s-%gkV-%g-Traj.csv" % (nmLinWid, linMat, umBlock, blkMat, e0, nTraj)
strOutFile = outDir + "/" + basFile
f=open(strOutFile, 'w')
strLine = hdr + '\n'
f.write(strLine)
for i in range(iCount):
strLine = "%.3f" % lX[i] + ","
strLine = strLine + "%.5f" % lKlin[i] + ","
strLine = strLine + "%.5f" % lKblk[i] + "\n"
f.write(strLine)
f.close()
def simLineInMatrix(lin, linMat, blk, blkMat, nmLinWid, umBlock, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True, nTraj=100, sf=True, bf=True, iDigits=5, bVerbose=False, xtraParams={}):
"""simLineInMatrix(lin, linMat, blk, blkMat, nmLinWid, umBlock, nPts,
trs, outDir, hdr, det, e0, lt, pc, withPoisson=True, nTraj=nTraj,
sf=True, bf=True, iDigits=5, bVerbose=False, xtraParams={})
Simulate a line of width `nmLinWid' nm at the center of a block of
`umBlock' microns. The line is of material `lin' with a name `linMat'.
The block is of material `blk' with a name `blkMat'.
We analyze an list `trs' of transitions, writing the K-ratios to a
.csv file with a header `hdr'. We use the detector `det', voltage `e0'
(kV) and live time `lt' sec and probe current `pc' nA. This will
compute the standard spectra, compute the spectra for nPts+1 from
-nPts/2 ... 0 ...nPts/2 times the block size. It will then compute the
K-ratios for each spectrum and write them to a file `name' in outDir
with a header `hdr' that matches the transition order.
"""
# order is order of trs..
sc = 1.0e-6 # scale from microns to meters for positions
lX = [] # an array for postions
lKlin = [] # an array for the K-ratio of the line
lKblk = [] # an array for the K-ratio of the block. Title correspond to hdr string
# start clean
dt2.DataManager.clearSpectrumList()
# create the standards
linStd = simulateBulkStandard(lin, linMat, det, e0, lt, pc, withPoisson=True, nTraj=nTraj, sf=True, bf=True, xtraParams={})
dt2.display(linStd)
blkStd = simulateBulkStandard(blk, blkMat, det, e0, lt, pc, withPoisson=True, nTraj=nTraj, sf=True, bf=True, xtraParams={})
dt2.display(blkStd)
lStd = {"El":dt2.element(linMat), "Spc":linStd}
bStd = {"El":dt2.element(blkMat), "Spc":blkStd}
stds = [lStd, bStd] # note: put the transitions in this order
iCount = 0
for x in range(-nPts/2, (nPts/2)+1, 1):
xv = sc*x*umBlock/nPts
lX.append(round(x*umBlock/nPts, iDigits))
monte=nm.MonteCarloSS()
monte.setBeamEnergy(epq.ToSI.keV(e0))
# use a 1 nm probe
beam=nm.GaussianBeam(1.0e-9)
monte.setElectronGun(beam)
beam.setCenter([xv, 0.0,-0.05])
# createBlock(double[] dims, double[] point, double phi, double theta, double psi)
# createBlock - Create a block of:
# dimensions specified in dims,
# centered at point,
# then rotated by the euler angles phi, theta, psi.
block = nm.MultiPlaneShape.createBlock([umBlock*1.0e-6, umBlock*1.0e-6, umBlock*1.0e-6],[0.0,0.0, 0.5*umBlock*1.0e-6],0.0,0.0,0.0)
matrix = monte.addSubRegion(monte.getChamber(), blk, block)
monte.addSubRegion(matrix, lin, nm.MultiPlaneShape.createBlock([1.0e-9*nmLinWid, umBlock*1.0e-6, umBlock*1.0e-6],[0.0, 0.0, 0.5*umBlock*1.0e-6],0.0,0.0,0.0))
det.reset()
# Add event listeners to model characteristic radiation
chXR = nm3.CharacteristicXRayGeneration3.create(monte)
xrel = nm3.XRayTransport3.create(monte, det, chXR)
brXR = nm3.BremsstrahlungXRayGeneration3.create(monte)
brem = nm3.XRayTransport3.create(monte, det, brXR)
fxg3 = nm3.FluorescenceXRayGeneration3.create(monte, chXR)
chSF = nm3.XRayTransport3.create(monte, det, fxg3)
brSF = nm3.XRayTransport3.create(monte, det, nm3.FluorescenceXRayGeneration3.create(monte, brXR))
# here is where we run the simulation
monte.runMultipleTrajectories(nTraj)
spec = det.getSpectrum((lt*pc*1.0e-9) / (nTraj * epq.PhysicalConstants.ElectronCharge))
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.FaradayEnd, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
spcName = "x = %.3f um" % x
epq.SpectrumUtils.rename(spec, spcName)
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
# display(spec)
a = jmg.compKRs(spec, stds, trs, det, e0)
iCount += 1
print(iCount)
lKlin.append(round(a[0], iDigits))
lKblk.append(round(a[1], iDigits))
basFile ="%gnm-%s-in-%gum-%s-%gkV-%g-Traj.csv" % (nmLinWid, linMat, umBlock, blkMat, e0, nTraj)
strOutFile = outDir + "/" + basFile
f=open(strOutFile, 'w')
strLine = hdr + '\n'
f.write(strLine)
for i in range(iCount):
strLine = "%.5f" % lX[i] + ","
strLine = strLine + "%.5f" % lKlin[i] + ","
strLine = strLine + "%.5f" % lKblk[i] + "\n"
f.write(strLine)
f.close()
msg = "Simulating %g nm C on Fe3C at %g kV %g traj" % (tc, e0, nTraj)
print(msg)
spc = sim_amc_coated_mat(fe3c, det, e0, nTraj, lt=lt, pc=pc, tc=tc)
display(spc)
sName = "%g-nm-C-on-Fe3C-%g-kV-%g-traj" % (tc, e0, nTraj)
fi = basePath + "/"
fi += sName
fi += ".msa"
if bSaveSpc == True:
spc.save(fi)
endCycle = time.time()
delta = (endCycle - startCycle) / 60
tod = datetime.datetime.now().time()
msg = "C layer %g of %g required %.3f min %s" % (i, nSpec, delta, tod)
print msg
res = jmg.compKRs(spc, stds, trs, det, e0)
if (bVerbose):
print(res)
kc = res[0]
kcMu = kc[0]
if (bVerbose):
print(kcMu)
kfe = res[1]
kfeMu = kfe[0]
if (bVerbose):
print(kfeMu)
print(kc)
print(kfe)
lNmC.append(tc)
lkC.append(kcMu)