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)
sim = mc3.simulate(mix, det, e0, dose, True,
nTraj, True, True, xtraParams)
fmtS = "Admiralty-Brass-at-%g-kV"
sName = fmtS % (e0)
sim.rename(sName)
sim.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
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)
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 = {}
al2o3.setName("Al2O3")
c = epq.Material(epq.Composition([epq.Element.C], [1.0]),
epq.ToSI.gPerCC(2.62))
c.setName("C")
xrts = [transition("Al K-L3"), transition("O K-L3"), transition("C K-L3")]
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, imgSizePx))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm * 1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSizePx))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.sphere(al2o3,
radUm * 1.0e-6,
det,
e0,
withPoisson=True,
nTraj=nTraj,
dose=pc * lt,
sf=True,
bf=True,
substrate=c,
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))
print(xtraParams)
fmtS = "%g-nm-C-on-EagleXG-at-%g-kV"
print("Starting simulation")
multiLaySim = mc3.multiFilm(layers, det, e0, True, nTraj, dose, True, True,
xtraParams)
sName = fmtS % (tCNm, e0)
multiLaySim.rename(sName)
multiLaySim.setAsStandard(eagleXG)
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)
print(trs)
# create samples consisting of silver film on steel (316H) substrate
film = {}
film[1] = [ag , 0.000000020],[s316H, 0.000010] # 0.000005000 = 5 um 0.000010 = 10um Configuring multi-layers composition and thickness
film[2] = [ag , 0.000000015],[s316H, 0.000010] # 0.000000050 = 0.05 um
film[3] = [ag , 0.000000010],[s316H, 0.000010]
xtraP = {}
xtraP = {"Characteristic Accumulator":True, "Char Fluor Accumulator":True, "Brem Fluor Accumulator":True}
# outpathoutPath = "/Users/jrminter/Documents/git/dtsa2Scripts/ben-buse/out/"
xtraP.update(mc3.configureOutput(outPath))
xtraP.update(mc3.configurePhiRhoZ(1.5*range))
xtraP.update(mc3.configureEmissionImages(trs, 1.5*range, size = 512))
xtraP.update(mc3.configureTrajectoryImage(1.5*range, size = 512))
resF = {}
for fil in film:
extension = str(film[fil][0])
extension = extension.replace("[","")
extension = extension.replace("]","")
extension = extension.replace(",","")
# pathloc = 'O:\Documents\PFE_Data\Users\Charles_Younes\\041115_CarbonInSteel\\dtsa2repeat7_' + extension # Change to output folder
xtraP.update(mc3.configureOutput(outPath))
print xtraP
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)
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))
"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))
