def simSpc(mat, e0, det, dose, ntraj, simDir):
"""
simSpc(mat, e0, det, dose, ntraj, simDir)
simulate a spectrum from a material and write it out.
"""
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(mat, det, e0, dose, True,
nTraj, True, True, xtraParams)
fmtS = "%s-at-%g-kV"
sName = fmtS % (mat.getName(), e0)
spc.rename(sName)
spc.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
return spc
def simSpc(mat, e0, det, dose, ntraj, simDir):
"""
simSpc(mat, e0, det, dose, ntraj, simDir)
simulate a spectrum from a material and write it out.
"""
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(mat, det, e0, dose, True, nTraj, True, True, xtraParams)
fmtS = "%s-at-%g-kV"
sName = fmtS % (mat.getName(), e0)
spc.rename(sName)
spc.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
return spc
def simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0, ctd=True):
"""simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
ctd - Boolean (True) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
cu = material("Cu", density=8.92)
a = jm3.simBulkStd(cu, det, 20.0, 100, 100, 1.0)
a.display()
"""
dose = pc * lt # na-sec"
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
sim = mc3.simulate(mat,
det,
e0,
dose,
withPoisson=True,
nTraj=nTraj,
sf=True,
bf=True,
xtraParams=xtraParams)
sName = "%s-%g-kV" % (mat, e0)
sim.rename(sName)
sim.setAsStandard(mat)
return sim
def simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0, ctd=True):
"""simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
ctd - Boolean (True) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
cu = material("Cu", density=8.92)
a = jm3.simBulkStd(cu, det, 20.0, 100, 100, 1.0)
a.display()
"""
dose = pc * lt # na-sec"
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
sim = mc3.simulate(mat, det, e0, dose, withPoisson=True, nTraj=nTraj,
sf=True, bf=True, xtraParams=xtraParams)
sName = "%s-%g-kV" % (mat, e0)
sim.rename(sName)
sim.setAsStandard(mat)
return sim
def simulate_spectrum(mat, e0, det, nTraj, dose, spcDir):
"""
simulate_spectrum(mat, e0, det, nTraj, dose, spcDir)
"""
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(mat, det, e0, dose, True, nTraj, True, True, xtraParams)
sName = "%s std-%g-kV" % (mat.getName(), e0)
spc.rename(sName)
spc.setAsStandard(mat)
spc.display()
# Save the spectra if NTraj > 500
if nTraj > 500:
fi = spcDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
return (spc)
def uncoatedSimBulkStd(mat,
det,
e0,
nTraj,
outPath,
dim=5.0e-6,
lt=100,
pc=1.0,
emiSize=512):
"""
uncoatedSimBulkStd(mat, det, e0, nTraj, outPath,
dim=5.0e-6, lt=100, pc=1.0, emiSize=512)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should
have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
outPath - string
The path to the directory for output
dim - float (5.0e-6)
The size of the emission images in um
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
emiSize - int (default 512)
The width and depth of the emission images.
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.jmMC3 as jm3
outPath = "path/to/yours/spc"
cu = material("Cu", density=8.92)
det = findDetector("Si(Li)")
a = jm3.uncoatedSimBulkStd(cu, det, 15.0, 100, outPath,
dim=5.0e-6, lt=100,
pc=1.0, emiSize=512)
a.display()
"""
start = time.time()
strMat = mat.getName()
dose = pc * lt # na-sec"
# specify the transitions to generate
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
# At 20 kV the images are best at 2.0e-6
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, dim, emiSize))
xtraParams.update(mc3.configurePhiRhoZ(dim))
xtraParams.update(mc3.configureTrajectoryImage(dim, emiSize))
xtraParams.update(mc3.configureVRML(nElectrons=100))
xtraParams.update(mc3.configureOutput(outPath))
print("Output sent to %s") % (outPath)
sim = mc3.simulate(mat, det, e0, lt * pc, True, nTraj, True, True,
xtraParams)
sName = "%s-%g-kV" % (strMat, e0)
sim.rename(sName)
sim.setAsStandard(mat)
sim.display()
end = time.time()
delta = end - start
msg = "This simulation required %.f sec" % (delta)
print(msg)
msg = " %.f min" % (delta / 60.0)
print(msg)
msg = " %.f hr" % (delta / 360.0)
print("")
return (sim)
def simCtdOxOnSi(det, e0, nTraj, lt=100, pc=1.0, tox=10.0, tc=20.0):
"""
simCtdOxOnSi(det, e0, nTraj, lt=100, pc=1.0, tox = 10.0, tc=20.0)
Use mc3 multilayer simulation to simulate a C-ctd silicon specimen
with a native oxide layer.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
tox - float (10.0)
The thickness of the native oxide in nm
tc - float (20.0)
C thickness in nm
Returns
-------
sim - DTSA scriptable spectrum
The simulated spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Si(Li)")
a = jm3.simCtdOxOnSi(det, 3.0, 100, 100, 1.0, 10.0, 20.0)
a.display()
"""
c = dt2.material("C", density=2.1)
si = dt2.material("Si", density=2.329)
sio2 = dt2.material("SiO2", density=2.65)
dose = pc * lt # na-sec"
layers = [[c, tc * 1.0e-9], [sio2, tox * 1.0e-9], [si, 50.0e-6]]
xrts = []
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(sio2, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
sim = mc3.multiFilm(layers,
det,
e0,
withPoisson=True,
nTraj=nTraj,
dose=dose,
sf=True,
bf=True,
xtraParams=xtraParams)
sName = "%g-nm-C-on-%g-nm-SiO2-on-Si-%g-kV-%g-Traj" % (tc, tox, e0, nTraj)
sim.rename(sName)
return sim
"SnO2": 0.0015215,
"BaO": 0.0012188,
"Fe2O3": 0.0005078,
"Sb2O3": 0.0004635,
"As2O3": 0.0003145,
"ZrO2": 0.0002938,
"TiO2": 0.0002540
},
density=2.36,
name="Eagle XG")
layers = [[c, tCNm * 1.0e-9], [eagleXG, 50.0e-6]]
xrts = []
trs = mc3.suggestTransitions(eagleXG, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm * 1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
# coating = False
# define materials
crocoite = material("PbCrO4", density=6.0)
crocoite.setName("Crocoite")
si = material("Si", density=2.3290)
k227 = epq.Material(
epq.Composition([epq.Element.O, epq.Element.Si, epq.Element.Pb],
[0.1640, 0.0934, 0.7246]), epq.ToSI.gPerCC(4.0))
k227.setName("k227")
# Start with k227
xrts = []
trs = mc3.suggestTransitions(k227, e0)
for tr in trs:
xrts.append(tr)
print(trs)
spc_k227 = jm3.simBulkStd(k227, det, e0, nTraj, 100, 1.0, False)
spc_k227.display()
spc_k227.rename("k227-5kV")
spc_k227.setAsStandard(k227)
fi = datDir + "/spc_k227.msa"
print(fi)
if (bSaveSpc):
spc_k227.save(fi)
# Next Si
os.chdir(wd)
pyrDir = wd + "/sim-C-on-Cu-w-Img Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
# start clean
DataManager.clearSpectrumList()
# create the materials
c = epq.Material(epq.Composition([epq.Element.C], [1.0],"C"), epq.ToSI.gPerCC(2.25))
cu = epq.Material(epq.Composition([epq.Element.Cu],[1.0],"Cu"), epq.ToSI.gPerCC(8.96))
# define the desired transitions
xrts=mc3.suggestTransitions("CCu")
# set up the extra parameters
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=charF, charFluorAccum=charF, bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
print(xtraParams)
# treat the substrate as 10 um C
sLay = [[c, tNmC/1.0e9], [cu, 10.0/1.0e6]]
l_mfs = [0.3872, 0.0794, 0.187, 0.1072, 0.1049, 0.0006, 0.1343]
k309 = jmg.create_material_from_mf(l_comps, l_mfs, 2.6, "K309")
si = material("Si", density=2.32)
caf2 = material("CaF2", density=3.18)
fe = material("Fe", density=7.874)
ti = material("Ti", density=4.506)
zn = material("Zn", density=7.14)
baf2 = material("BaF2", density=4.89)
al2o3 = material("Al2O3", density=3.95)
xrts = []
trs = mc3.suggestTransitions(k309, e0)
for tr in trs:
xrts.append(tr)
k309_spc = jm3.simBulkStd(k309, det, e0, nTraj, lt, pc, True)
k309_spc.display()
si_spc = jm3.simBulkStd(si, det, e0, nTraj, lt, pc, True)
si_spc.display()
caf2_spc = jm3.simBulkStd(caf2, det, e0, nTraj, lt, pc, True)
caf2_spc.display()
fe_spc = jm3.simBulkStd(fe, det, e0, nTraj, lt, pc, True)
fe_spc.display()
# tmp = u"MC simulation of a [%0.2f,%0.2f,%0.2f] micron block of %s%s coated with %0.2f microns of %s at %0.1f keV%s%s" % (width * 1.0e6, width * 1.0e6, height * 1.0e6, mat, (" on %s" % substrate if substrate else ""), coating, e0, (" + CSF" if sf else ""), (" + BSF" if bf else ""))
params = {"Substrate": substrate, "Width" : width, "Height" : height, "Material" : mat, "Coating" : coating, "Thickness" : thickness}
return mc3.base(det, e0, withPoisson, nTraj, dose, sf, bf, tmp, buildBlock, params, xtraParams)
pet = epq.Material(epq.Composition([epq.Element.C,epq.Element.H,epq.Element.O],[0.62502,0.04196,0.069042]),epq.ToSI.gPerCC(1.37))
pet.setName("PET")
al2o3 = epq.Material(epq.Composition([epq.Element.Al,epq.Element.O],[0.5293,0.4707]),epq.ToSI.gPerCC(3.95))
al2o3.setName("Al2O3")
ag = epq.Material(epq.Composition([epq.Element.Ag],[1.0],"Ag"), epq.ToSI.gPerCC(11.9))
ag.setName("Ag")
# start clean
DataManager.clearSpectrumList()
# define the desired transitions
xrts=mc3.suggestTransitions("COAlAg")
# print(xrts)
# set up the extra parameters
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=charF, charFluorAccum=charF, bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
print(xtraParams)
spc = coatedOverBlock(ag, tBlk*1.0e-6, wBlk*1.0e-6, al2o3, tFlm*1.0e-6, pet, det, e0=e0, withPoisson=True, nTraj=nTraj, dose=dose, sf=charF, bf=bremF, xtraParams=xtraParams)
display(spc)
relPrj = "/dtsa2Scripts/"
simDir = gitDir + relPrj + "/mc3AnodizedAl/"
jmg.ensureDir(simDir)
imgSize = 512 # pixel size for images
imgSzUm = 5.0 # image size in microns
vmrlEl = 100 # number of el for VMRL
wd = simDir
os.chdir(wd)
pyrDir = wd + "/sim-multifilm-on-sub Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
xrts=mc3.suggestTransitions("AlO")
print(xrts)
for tr in xrts:
print(tr.getSiegbahnName())
for tr in xrts:
print(tr.getIUPACName())
# set up the extra parameters
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=True, charFluorAccum=True, bremFluorAccum=True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
pyrDir = wd + "/sim-C-on-Cu-w-Img Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
# start clean
DataManager.clearSpectrumList()
# create the materials
c = epq.Material(epq.Composition([epq.Element.C], [1.0], "C"),
epq.ToSI.gPerCC(2.25))
cu = epq.Material(epq.Composition([epq.Element.Cu], [1.0], "Cu"),
epq.ToSI.gPerCC(8.96))
# define the desired transitions
xrts = mc3.suggestTransitions("CCu")
# set up the extra parameters
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(xrts,
charAccum=charF,
charFluorAccum=charF,
bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm * 1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
dose = pc * lt # na-sec"
# should not need to change below here
homDir = os.environ['HOME']
homDir = homDir.replace('\\', '/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/utility"
outDir = homDir + "/Documents/git/dtsa2Scripts/html"
rptDir = wrkDir + '/testMC3AdmiraltyBrass Results/'
simDir = homDir + "/Documents/git/dtsa2Scripts/sim-Admiralty-Brass"
dt2c.ensureDir(simDir)
DataManager.clearSpectrumList()
xrts = []
trs = mc3.suggestTransitions(mix, e0)
for tr in trs:
xrts.append(tr)
# print(xrts)
xtraParams = {}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm * 1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
print(xtraParams)
caf2 = material("CaF2", density= 3.18)
# start with the 'unknown'
layers = [ [c, tNmC*1.0e-9],
[k411, 50.0e-6]
]
# multiFilm(layers, det, e0=20.0, withPoisson=True,
# nTraj=defaultNumTraj, dose=defaultDose,
# sf=defaultCharFluor, bf=defaultBremFluor,
# xtraParams=defaultXtraParams)
xrts = []
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(k411, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm*1.0e-6, resln))
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
pet = epq.Material(
epq.Composition([epq.Element.C, epq.Element.H, epq.Element.O],
[0.62502, 0.04196, 0.069042]), epq.ToSI.gPerCC(1.37))
pet.setName("PET")
al2o3 = epq.Material(
epq.Composition([epq.Element.Al, epq.Element.O], [0.5293, 0.4707]),
epq.ToSI.gPerCC(3.95))
al2o3.setName("Al2O3")
ag = epq.Material(epq.Composition([epq.Element.Ag], [1.0], "Ag"),
epq.ToSI.gPerCC(11.9))
ag.setName("Ag")
# start clean
DataManager.clearSpectrumList()
# define the desired transitions
xrts = mc3.suggestTransitions("COAlAg")
# print(xrts)
# set up the extra parameters
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(xrts,
charAccum=charF,
charFluorAccum=charF,
bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm * 1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
def fullSimBulkStd(mat, ctg, ctgThickNm, det, e0, nTraj, outPath,
dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False):
"""
fullSimBulkStd(mat, ctg, ctgThickNm, det, e0, nTraj, outPath,
dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should
have a useful name.
ctg - a dtsa2 material for the coating
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
outPath - string
The path to the directory for output
dim - float (5.0e-6)
The size of the emission images
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
emiSize - int (default 512)
The width and depth of the emission images.
ctd - Boolean (False) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.mcSimulate3 as mc3
det = findDetector("Oxford p4 05eV 4K")
cu = material("Cu", density=8.92)
outPath = "C:/Users/johnr/Documents/git/dtsa2Scripts/ben-buse/out"
a = fullSimBulkStd(cu, det, 15.0, 100, outPath,
dim=5.0e-6, lt=100,
pc=1.0, emiSize=512, ctd=False)
a.display()
"""
strCtg = ctg.getName()
strMat = mat.getName()
dose = pc * lt # na-sec"
# specify the transitions to generate
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(ctg, e0)
for tr in trs:
xrts.append(tr)
# At 20 kV the images are best at 2.0e-6
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, 2.0e-6, 512))
xtraParams.update(mc3.configurePhiRhoZ(2.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(2.0e-6, 512))
xtraParams.update(mc3.configureVRML(nElectrons=100))
xtraParams.update(mc3.configureOutput(outPath))
print("Output sent to %s") % (outPath)
layers = [ [ctg, ctgThickNm*1.0e-9],
[mat, 1.0e-3]]
sim = mc3.multiFilm(layers, det, e0, withPoisson=True, nTraj=nTraj,
dose=dose, sf=True, bf=True, xtraParams=xtraParams)
sName = "%g-nm-%s-on-%s" % (tNmC, strCtg, strMat)
sim.rename(sName)
sim.setAsStandard(mat)
sim.display()
return(sim)
}, 1.16, 'Epon828')
det = findDetector("Probe")
# use a limited set for emission images
xrtsEI = [
transition("C K-L3"),
transition("Fe K-L3"),
transition("Fe L3-M5"),
transition("Ni K-L3"),
transition("Ni L3-M5")
]
xrts = []
trs = mc3.suggestTransitions(nbsNiFe, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(Epon828, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm * 1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(
mc3.configureEmissionImages(xrtsEI, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
def sim_amc_coated_mat(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0):
"""sim_amc_coated_mat(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0)
Use mc3 multilayer simulation to simulate an am-C-ctd specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
tc - float (20.0)
C thickness in nm
Returns
-------
sim - DTSA scriptable spectrum
The simulated spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
si = material("Si", density=2.3296)
a = jm3.simCarbonCoatedStd(mgo, det, 5.0, 100, 100, 1.0, 20.0)
a.display()
"""
dose = pc * lt # na-sec"
amc = material("C", density=1.35)
amcThickComment = "amC Thickness = %g nm %g trajectories" % (tc, nTraj)
layers = [[amc, tc * 1.0e-9], [mat, 50.0e-6]]
xrts = []
trs = mc3.suggestTransitions(amc, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
sim = mc3.multiFilm(layers,
det,
e0,
withPoisson=True,
nTraj=nTraj,
dose=dose,
sf=True,
bf=True,
xtraParams=xtraParams)
sName = "%g-nm-amC-on-%s-%g-kV" % (tc, mat, e0)
sim.rename(sName)
sim.getProperties().setTextProperty(epq.SpectrumProperties.SpectrumComment,
amcThickComment)
return sim
"As2O3" : 0.0003145,
"ZrO2" : 0.0002938,
"TiO2" : 0.0002540
},
density=2.36,
name="Eagle XG")
layers = [ [c, tCNm*1.0e-9],
[eagleXG, 50.0e-6]
]
xrts = []
trs = mc3.suggestTransitions(eagleXG, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm*1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
sim.rename(sName)
sim.setAsStandard(mat)
return sim
start = time.time()
DataManager.clearSpectrumList()
# define materials
b = material("B", density = 2.37)
bn = material("BN", density = 2.1)
aln = material("AlN", density = 3.26)
xrts = []
trs = mc3.suggestTransitions(b, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(aln, e0)
for tr in trs:
xrts.append(tr)
spc_b = simBulkStd(b, det, e0, nTraj, 100, 1.0, False)
spc_b.display()
spc_b.rename("B-5kV")
spc_b.setAsStandard(b)
fi = datDir + "/spc_b.msa"
print(fi)
if(bSaveSpc):
spc_b.save(fi)
"C" : 0.7440,
"O" : 0.1855,
"Cl" : 0.0030},
1.16,
'Epon828')
det = findDetector("Probe")
# use a limited set for emission images
xrtsEI = [transition("C K-L3"),
transition("Fe K-L3"), transition("Fe L3-M5"),
transition("Ni K-L3"), transition("Ni L3-M5")]
xrts = []
trs = mc3.suggestTransitions(nbsNiFe, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(Epon828, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm*1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrtsEI, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
# xtraParams.update(mc3.configureOutput(simDir))
defaultNumTraj = 1000
if 'defaultDose' not in globals():
defaultDose = 120.0
# start clean
DataManager.clearSpectrumList()
pet = epq.Material(epq.Composition([epq.Element.C,epq.Element.H,epq.Element.O],[0.62502,0.04196,0.069042]),epq.ToSI.gPerCC(1.37))
cu = epq.Material(epq.Composition([epq.Element.Cu],[1.0],"Cu"), epq.ToSI.gPerCC(8.96))
pd = epq.Material(epq.Composition([epq.Element.Pd],[1.0],"Pd"), epq.ToSI.gPerCC(11.9))
ag = epq.Material(epq.Composition([epq.Element.Ag],[1.0],"Ag"), epq.ToSI.gPerCC(10.5))
# define the desired transitions
xrts=mc3.suggestTransitions("COCuPdAg")
# print(xrts)
# set up the extra parameters
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=charF, charFluorAccum=charF, bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
print(xtraParams)
spc = jm3.triLayerLineOnSubstrate(pd, cu, ag, pet, tNmPd*1.0e-9, tNmCu*1.0e-9, tNmAg*1.0e-9, wUm*1.0e-06, lUm*1.0e-06, det, title, e0=e0, withPoisson=True, nTraj=nTraj, dose=dose, sf=charF, bf=bremF, xtraParams=xtraParams)
display(spc)
srm1155 = jmg.create_material_from_mf(l_comps, l_mfs, 7.97, "SRM1155")
c = material("C", density=2.267)
mn = material("Mn", density=7.43)
p = material("P", density=1.88)
s = material("S", density=2.0)
si = material("Si", density=2.32)
cu = material("Cu", density=8.96)
mo = material("Mo", density=10.2)
co = material("Co", density=8.86)
pb = material("Pb", density=11.34)
fe = material("Fe", density=7.874)
xrts = []
trs = mc3.suggestTransitions(srm1155, e0)
for tr in trs:
xrts.append(tr)
srm1155_spc = jm3.simBulkStd(srm1155, det, e0, nTraj, lt, pc, True)
srm1155_spc.setAsStandard(srm1155)
srm1155_spc.display()
srm1155_spc.save(srm1555_path)
"""
si_spc = jm3.simBulkStd(si, det, e0, nTraj, lt, pc, True)
si_spc.display()
caf2_spc = jm3.simBulkStd(caf2, det, e0, nTraj, lt, pc, True)
caf2_spc.display()
datDir = gitHomeDir + relPrj
print(gitHomeDir)
print(datDir)
start = time.time()
DataManager.clearSpectrumList()
# define materials
b = material("B", density=2.37)
bn = material("BN", density=2.1)
aln = material("AlN", density=3.26)
xrts = []
trs = mc3.suggestTransitions(bn, e0)
for tr in trs:
xrts.append(tr)
# def simulateBulkStandard(mat, name, det, e0, lt, pc, withPoisson=True, nTraj=100, sf=True, bf=True, xtraParams={}):
spc_b = jm3.simBulkStd(b, det, e0, nTraj, 100, 1.0, False)
spc_b.display()
spc_b.rename("B-5kV")
spc_b.setAsStandard(b)
fi = datDir + "/spc_b.msa"
print(fi)
if (bSaveSpc):
spc_b.save(fi)
spc_bn = jm3.simBulkStd(bn, det, e0, nTraj, 100, 1.0, False)
def fullSimBulkStd(mat, det, e0, nTraj, outPath, dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False):
"""
fullSimBulkStd(mat, det, e0, nTraj, outPath, dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
outPath - string
The path to the directory for output
dim - float (5.0e-6)
The size of the emission images
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
emiSize - int (default 512)
The width and depth of the emission images.
ctd - Boolean (False) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.mcSimulate3 as mc3
det = findDetector("Oxford p4 05eV 2K")
cu = material("Cu", density=8.92)
a = fullSimBulkStd(cu, det, 20.0, 100, 100, 1.0)
a.display()
"""
dose = pc * lt # na-sec"
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
mc3.configureEmissionImages(xrts, dim, emiSize)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, 5.0e-6, 512))
xtraParams.update(mc3.configurePhiRhoZ(5.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(5.0e-6, 512))
xtraParams.update(mc3.configureVRML(nElectrons=100))
xtraParams.update(mc3.configureOutput(outPath))
mc3.configureOutput(outPath)
print("Output sent to %s") % (outPath)
dose = lt*pc
sim = mc3.simulate(mat, det, e0, dose, withPoisson=True, nTraj=nTraj,
sf=True, bf=True, xtraParams=xtraParams)
sName = "%s-%g-kV" % (mat, e0)
sim.rename(sName)
sim.setAsStandard(mat)
sim.display()
fi = outPath + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
print(fi)
sim.save(fi)
return(sim)
Monte Carlo simulate a spectrum from a block shaped particle of the specified material (mat) and height (z in m) and width (x and y in m). \
The block and subtrate is coated in a material 'coating' of the specified thickness which fully encapsulates the particle and covers the substrate too."""
def buildBlock(monte, origin, buildParams):
height = buildParams["Height"]
width = buildParams["Width"]
subMat = buildParams["Substrate"]
mat = buildParams["Material"]
coating = buildParams["Coating"]
thickness = buildParams["Thickness"]
coatedCube = nm.MultiPlaneShape.createBlock([width+2.0*thickness, width+2.0*thickness, height+thickness], epu.Math2.plus(origin, [0.0, 0.0, 0.5 * (height+thickness)]), 0.0, 0.0, 0.0)
sr1=monte.addSubRegion(monte.getChamber(), coating, coatedCube)
cube = nm.MultiPlaneShape.createBlock([width, width, height], epu.Math2.plus(origin, [0.0, 0.0, thickness + 0.5 * height]), 0.0, 0.0, 0.0)
monte.addSubRegion(sr1, mat, cube)
monte.addSubRegion(monte.getChamber(), coating, nm.MultiPlaneShape.createFilm([0.0, 0.0, -1.0], epu.Math2.plus(origin, [0.0, 0.0, height+thickness]), thickness))
monte.addSubRegion(monte.getChamber(), subMat, nm.MultiPlaneShape.createSubstrate([0.0, 0.0, -1.0], epu.Math2.plus(origin, [0.0, 0.0, height+2.0*thickness])))
tmp = u"MC simulation of a [%0.2f,%0.2f,%0.2f] micron block of %s%s coated with %s at %0.1f keV%s%s" % (width * 1.0e6, width * 1.0e6, height * 1.0e6, mat, (" on %s" % substrate if substrate else ""), coating, e0, (" + CSF" if sf else ""), (" + BSF" if bf else ""))
params = {"Substrate": substrate, "Width" : width, "Height" : height, "Material" : mat, "Coating" : coating, "Thickness" : thickness}
return mc3.base(det, e0, withPoisson, nTraj, dose, sf, bf, tmp, buildBlock, params, xtraParams)
# Stuff you change....
substrate = material("Fe",8.0)
coating = material("Cu",7.0)
block = material("Al",3.0)
elements = "FeCuAl" # List the elements in the substrate, coating and block...
xrts=mc3.suggestTransitions(elements)
xp = mc3.configureEmissionImages(xrts,2.0e-6,512)
# xp.update(mc3.configureXRayAccumulators(xrts,charAccum=True,charFluorAccum=True,bremFluorAccum=False))
xp.update(mc3.configureTrajectoryImage(2.0e-6,512))
display(coatedBlock(block,0.1e-6,0.2e-6,coating,0.05e-6,substrate,d1,e0=20.0, nTraj=1000, xtraParams=xp))
spcDir = gitDir + '/dtsa2Scripts/spc/sim-raft-on-zno-on-si'
jmg.ensureDir(spcDir)
DataManager.clearSpectrumList()
start = time.time()
# define materials
zno = material("ZnO", density=5.61)
si = material("Si", density=2.33)
raft = material("C17H35O5S2P1", density=2.0)
raft.setName("RAFT polymer")
# specify the x-ray transitions
xrts = []
trs = mc3.suggestTransitions(zno, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(si, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(raft, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm*1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
def simCtdOxOnSi(det, e0, nTraj, lt=100, pc=1.0, tox = 10.0, tc=20.0):
"""
simCtdOxOnSi(det, e0, nTraj, lt=100, pc=1.0, tox = 10.0, tc=20.0)
Use mc3 multilayer simulation to simulate a C-ctd silicon specimen
with a native oxide layer.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
tox - float (10.0)
The thickness of the native oxide in nm
tc - float (20.0)
C thickness in nm
Returns
-------
sim - DTSA scriptable spectrum
The simulated spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
a = jm3.simCtdOxOnSi(det, 3.0, 100, 100, 1.0, 10.0, 20.0)
a.display()
"""
c = dt2.material("C", density=2.1)
si = dt2.material("Si", density=2.329)
sio2 = dt2.material("SiO2", density=2.65)
dose = pc * lt # na-sec"
layers = [ [ c, tc*1.0e-9],
[sio2, tox*1.0e-9],
[si, 50.0e-6] ]
xrts = []
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(sio2, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
sim = mc3.multiFilm(layers, det, e0, withPoisson=True, nTraj=nTraj,
dose=dose, sf=True, bf=True, xtraParams=xtraParams)
sName = "%g-nm-C-on-%g-nm-SiO2-on-Si-%g-kV-%g-Traj" % (tc, tox, e0, nTraj)
sim.rename(sName)
return sim
sf=True,
bf=True,
xtraParams={})
sName = "%g-nm-C-on-K497" % tNmC
k497Sim.rename(sName)
k497Sim.setAsStandard(k497)
k497Sim.display()
fi = spcDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
k497Sim.save(fi)
# Al2O3 Sim
al2o3 = material("Al2O3", 3.95)
layers = [[c, 2.0e-9], [al2o3, 50.0e-6]]
xrts = mc3.suggestTransitions(al2o3)
al2o3Sim = mc3.multiFilm(layers,
det,
e0,
withPoisson=True,
nTraj=nTraj,
dose=dose,
sf=True,
bf=True,
xtraParams={})
sName = "%g-nm-C-on-Al2O3" % tNmC
al2o3Sim.rename(sName)
al2o3Sim.setAsStandard(al2o3)
al2o3Sim.display()
fi = spcDir + "/"
fi += sName
si = material("Si", density=2.329)
fe = material("Fe", density=7.86)
caf2 = material("CaF2", density=3.18)
# start with the 'unknown'
layers = [[c, tNmC * 1.0e-9], [k411, 50.0e-6]]
# multiFilm(layers, det, e0=20.0, withPoisson=True,
# nTraj=defaultNumTraj, dose=defaultDose,
# sf=defaultCharFluor, bf=defaultBremFluor,
# xtraParams=defaultXtraParams)
xrts = []
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(k411, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm * 1.0e-6, resln))
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
# directories
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/utility"
prjDir = gitDir + relPrj
resDir = prjDir + '/sim-zno-on-si-4kV'
jmg.ensureDir(resDir)
rptDir = prjDir + '/sim-zno-on-si-4kV Results/'
DataManager.clearSpectrumList()
start = time.time()
zno = material("ZnO", density=5.61)
si = material("Si", density=2.33)
xrts = []
trs = mc3.suggestTransitions(zno, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# xtraParams.update(mc3.configureOutput(simDir))
spc_zno_std = mc3.simulate(zno, det, e0, dose, True, nTraj, True, True,
xtraParams)
sName = "ZnO std-%g-kV" % (e0)
spc_zno_std.rename(sName)
spc_zno_std.setAsStandard(zno)
spc_zno_std.display()
fi = resDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
os.chdir(wrkDir)
przDir = wrkDir + '/prz/'
# Save spectra in sim directory
jmg.ensureDir(przDir)
# jmg.ensureDir(rptDir)
det = findDetector("Oxford p4 05eV 4K")
e0 = 7 # kV
nSteps = e0*100 # steps
rho = 2.6 # sec
l_comps = [epq.Element.Al, epq.Element.Mg, epq.Element.P, epq.Element.O]
l_mfs = [ 0.06470, 0.06650, 0.32900, 0.5390]
k496 = jmg.create_material_from_mf(l_comps, l_mfs, 2.6, "K-496")
xrts = mc3.suggestTransitions(k496)
a = jmg.compPhiRhoZ(k496, det, e0, nSteps, xrts, alg=epq.PAP1991(), base="pap-prz", outdir=przDir)
# clean up cruft
# 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
print msg
def simCoatedSubstrate(mat, ctg, thNm, det, e0, nTraj, lt=100, pc=1.0):
"""simCoatedSubstrate(mat, ctg, thNm, det, e0, nTraj, lt=100, pc=1.0)
Use mc3 multilayer simulation to simulate an coated substrate specimen
This ONLY generates a spectrum
Parameters
----------
mat - a dtsa material for the substrate.
Note the material must have an associated density.
It should have a useful name.
ctg - a dtsa material for the coating
thNm - coating thickness in nm
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
tc - float (20.0)
C thickness in nm
Returns
-------
sim - DTSA scriptable spectrum
The simulated spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.jmMC3 as jm3
det = findDetector("Si(Li)")
sio2 = material("SiO2", 2.65)
si = material("Si", 2.3296)
a = jm3.simCoatedSubstrate(si, sio2, 10.0, det, e0, nTraj, 100, 1.0)
a.display()
"""
dose = pc * lt # na-sec"
layers = [[ctg, thNm * 1.0e-9], [mat, 50.0e-6]]
xrts = []
trs = mc3.suggestTransitions(ctg, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
sim = mc3.multiFilm(layers, det, e0, True, nTraj, dose, True, True,
xtraParams)
sName = "%g-nm-%s-on-%s-%g-kV" % (thNm, ctg, mat, e0)
sim.rename(sName)
return sim
def sim_amc_coated_mat(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0):
"""sim_amc_coated_mat(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0)
Use mc3 multilayer simulation to simulate an am-C-ctd specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
tc - float (20.0)
C thickness in nm
Returns
-------
sim - DTSA scriptable spectrum
The simulated spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
si = material("Si", density=2.3296)
a = jm3.simCarbonCoatedStd(mgo, det, 20.0, 100, 100, 1.0, 20.0)
a.display()
"""
dose = pc * lt # na-sec"
amc = material("C", density=1.35)
amcThickComment = "amC Thickness = %g nm %g trajectories" % (tc, nTraj)
layers = [ [amc, tc*1.0e-9],
[mat, 50.0e-6]
]
xrts = []
trs = mc3.suggestTransitions(amc, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
sim = mc3.multiFilm(layers, det, e0, withPoisson=True, nTraj=nTraj,
dose=dose, sf=True, bf=True, xtraParams=xtraParams)
sName = "%g-nm-amC-on-%s-%g-kV" % (tc, mat, e0)
sim.rename(sName)
sim.getProperties().setTextProperty(epq.SpectrumProperties.SpectrumComment, amcThickComment)
return sim
def simCarbonCoatedStd(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0):
"""simCarbonCoatedStd(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0)
Use mc3 multilayer simulation to simulate a C-ctd standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
tc - float (20.0)
C thickness in nm
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Si(Li)")
mgo = material("MgO", density=3.58)
a = jm3.simCarbonCoatedStd(mgo, det, 20.0, 100, 100, 1.0, 20.0)
a.display()
"""
dose = pc * lt # na-sec"
c = dt2.material("C", density=2.1)
layers = [[c, tc * 1.0e-9], [mat, 50.0e-6]]
xrts = []
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
sim = mc3.multiFilm(layers,
det,
e0,
withPoisson=True,
nTraj=nTraj,
dose=dose,
sf=True,
bf=True,
xtraParams=xtraParams)
sName = "%g-nm-C-on-%s-%g-kV-%g-Traj" % (tc, mat, e0, nTraj)
sim.rename(sName)
sim.setAsStandard(mat)
return sim
DataManager.clearSpectrumList()
start = time.time()
sio2 = material("SiO2", density=2.196)
# sio = material("SiO", density=2.13)
# Read standard
fi = spcDir + "/SiO2 std.msa"
spc_sio2_std = readSpectrum(fi)
spc_sio2_std.display()
lDoseUnk = [50, 100, 200, 500, 1000, 2500, 5000]
xrts = []
trs = mc3.suggestTransitions(sio2, e0)
for tr in trs:
xrts.append(tr)
stds = { element("O"): spc_sio2_std, element("Si"): spc_sio2_std }
qus = multiQuant(det, e0, stds, {})
for doseUnk in lDoseUnk:
sName = "SiO Unk %g nA-sec.msa" % (doseUnk)
fi = spcDir + "/" + sName
spc_sio_unk = readSpectrum(fi)
spc_sio_unk.display()
res = qus.compute(spc_sio_unk)
print(sName)
print("Weight Fraction")
SRM482A = material("Au",rhoAu)
SRM482B = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.801,0.198],"Au80Cu20"),epq.ToSI.gPerCC(0.8*rhoAu+0.2*rhoCu))
SRM482C = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.603,0.396],"Au60Cu40"),epq.ToSI.gPerCC(0.6*rhoAu+0.4*rhoCu))
SRM482D = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.401,0.599],"Au40Cu60"),epq.ToSI.gPerCC(0.4*rhoAu+0.6*rhoCu))
SRM482E = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.201,0.798],"Au20Cu80"),epq.ToSI.gPerCC(0.2*rhoAu+0.8*rhoCu))
SRM482F = material("Cu",rhoCu)
SRM482 = ( SRM482A, SRM482B, SRM482C, SRM482D, SRM482E, SRM482F, )
range = electronRange(SRM482A,e0,density=None)
xtraP = {}
xtraP.update(mc3.configureOutput(DefaultOutput))
xtraP.update(mc3.configurePhiRhoZ(1.5*range))
xtraP.update(mc3.configureEmissionImages(mc3.suggestTransitions(SRM482C,e0), 1.5*range, size = 512))
xtraP.update(mc3.configureTrajectoryImage(1.5*range, size = 512))
specs = {}
for mat in SRM482:
if terminated:
break
specs[mat] = mc3.simulate(mat, det,e0=e0, nTraj=nE, dose=500.0, sf=True, bf=True,xtraParams=xtraP)
specs[mat].save("%s/%s.msa" % ( DefaultOutput, specs[mat] ))
specs[mat].display()
unks = ( specs[SRM482B], specs[SRM482C], specs[SRM482D], specs[SRM482E] )
stds = { "Au" : specs[SRM482A], "Cu" : specs[SRM482F] }
res = {}
pyrDir = wd + "/sim-vert-layers Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
# start clean
DataManager.clearSpectrumList()
pet = epq.Material(epq.Composition([epq.Element.C,epq.Element.H,epq.Element.O],[0.62502,0.04196,0.069042]),epq.ToSI.gPerCC(1.37))
cu = epq.Material(epq.Composition([epq.Element.Cu],[1.0],"Cu"), epq.ToSI.gPerCC(8.96))
pd = epq.Material(epq.Composition([epq.Element.Pd],[1.0],"Pd"), epq.ToSI.gPerCC(11.9))
# define the desired transitions
# xrts = [epq.XRayTransitionSet(epq.Element.Pd, epq.XRayTransitionSet.L_FAMILY), epq.XRayTransitionSet(epq.Element.Cu, epq.XRayTransitionSet.L_FAMILY)]
xrts=mc3.suggestTransitions("CuPd")
print(xrts)
for tr in xrts:
print(tr.getSiegbahnName())
for tr in xrts:
print(tr.getIUPACName())
# set up the extra parameters
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=charF, charFluorAccum=charF, bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
dose = pc * lt # na-sec"
# should not need to change below here
homDir = os.environ['HOME']
homDir = homDir.replace('\\','/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/utility"
outDir = homDir + "/Documents/git/dtsa2Scripts/html"
rptDir = wrkDir + '/testMC3AdmiraltyBrass Results/'
simDir = homDir + "/Documents/git/dtsa2Scripts/sim-Admiralty-Brass"
dt2c.ensureDir(simDir)
DataManager.clearSpectrumList()
xrts = []
trs = mc3.suggestTransitions(mix, e0)
for tr in trs:
xrts.append(tr)
# print(xrts)
xtraParams={}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm*1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6,
imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
"Height": height,
"Material": mat,
"Coating": coating,
"Thickness": thickness
}
return mc3.base(det, e0, withPoisson, nTraj, dose, sf, bf, tmp, buildBlock,
params, xtraParams)
# Stuff you change....
substrate = material("Fe", 8.0)
coating = material("Cu", 7.0)
block = material("Al", 3.0)
elements = "FeCuAl" # List the elements in the substrate, coating and block...
xrts = mc3.suggestTransitions(elements)
xp = mc3.configureEmissionImages(xrts, 2.0e-6, 512)
# xp.update(mc3.configureXRayAccumulators(xrts,charAccum=True,charFluorAccum=True,bremFluorAccum=False))
xp.update(mc3.configureTrajectoryImage(2.0e-6, 512))
display(
coatedBlock(block,
0.1e-6,
0.2e-6,
coating,
0.05e-6,
substrate,
d1,
e0=20.0,
nTraj=1000,
xtraParams=xp))
