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General EDS Issues / Trilayer simulation with Penepma from CalcZAF
« Last post by jrminter on Today at 11:21:57 am »
Probeman, your suggestion to try this with CalcZAF intrigued me.  Farhuit's example was really a tri-layer system with Ir on Ag on silica. As I read the examples on the penepma part of the forum I saw your edits to do a trilayer system from a bilayer simulation where one layer was air. I tried to adapt your method with the input file attached below (Ir-250-on-Ag-150-on-Silica.in). I used standard pure elements from the standards database for Ir and Ag and a SiO2 standard. I renamed the mat files to "Ir.mat", "Ag.mat", and "SiO2.mat" because it made the simulation a bit more readable. I created a trilayer.geo file (tl_250_150nm.geo) based on your example (attached below). I ran the simulation for an hour. I have done this before on bilayers and the noise wasn't as bad (see the png). I thought this capability would complement the simuations I do with DTSA for EDS...

I'd appreciate it if you would take a look at my edits to the '.in' and '.geo' files to see if anything strikes you as wrong. Thought another pair of eyes would be helpful before I set up a 24 hour run to see if the problems is too few counts...

Thanks for all your work on this...

Best regards,
John
2
And then there's another thing to consider which may or may not be possible for you (where are you again?).  When acquiring standards in Probe for EPMA the default is to acquire all the elements one is analyzing for in all the standards. One can always check the "quick standards" checkbox later to save time once the elements/backgrounds/interferences setup is finalized, but at least to begin with, one really should measure all the elements one is measuring in all of the standards in the run.

Why is this useful?  Because in PFE one can then "analyze" each primary and secondary (and MAN) standard as an unknown, and then one can ascertain whether they have been successful or not in measuring, first, the minor or major elements in any standard that is *not* a primary standard, and second, for our current purposes, any elements that are denoted as zero in those secondary standards.  For example, one might be using synthetic MnO as a Mn standard. In this case, by measuring all our elements (including say Fe), we can evaluate whether we can measure zero Fe in the presence of Mn. Of course we will immediately learn that there is a Mn Kb interference on Fe K which needs to be dealt with, but the good news is that we've *already* calibrated this spectral interference in measuring all our elements in that standard matrix! One simply then assigns the interference with a few mouse clicks and you're good to good (for trace Fe in the presence of Mn at least!).

As another example one might be analyzing the following elements for an amphibole (this is actually a student run for traces in apatite but it makes the point):

ELEM:    ca ka    p ka    s ka   al ka   fe ka   as ka   ba la    k ka
ELEM:    mn ka   na ka   sr la    f ka   sm la   nd la   cl ka    y la
ELEM:    eu la   gd la   mg ka   la la   ce la   si ka

The standards specified for this run were:

160 NBS K-412 mineral glass
285 Ca10(PO4)6Cl2 (halogen corrected)
327 Anhydrite (CaSO4) UC # 5555
336 Nepheline (partial anal.)
835 BaF2 (barium fluoride)
1001 CePO4 (USNM 168484)
1004 EuPO4 (USNM 168487)
1005 GdPO4 (USNM 168488)
1007 LaPO4 (USNM 168490)
1009 NdPO4 (USNM 168492)
1011 SmPO4 (USNM 168494)
1015 YbPO4 (USNM 168498)
1016 YPO4 (USNM 168499)
25 MnO synthetic
251 Strontium titanate (SrTiO3)
662 GaAs (synthetic)

Now once the standards are acquired, we can "analyze" them as unknowns in PFE to check for backgrounds, absorption edges, interferences, etc.  As you know, problems with the background usually manifest themselves as negative concentrations, while problems with interferences usually reveal themselves as concentrations statistically above zero (assuming the trace element in the standard is at zero concentration).  So here is an example of our synthetic chlor-apatite being analyzed as a secondary standard:

St  285 Set   3 Ca10(PO4)6Cl2 (halogen corrected), Results in Elemental Weight Percents
 
ELEM:       Ca       P       S      Al      Fe      As      Ba       K
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL
BGDS:      LIN     EXP     LIN     LIN     LIN     EXP     LIN     LIN
TIME:    25.00    8.00   25.00   25.00   30.00   20.00   30.00   30.00
BEAM:    30.14   30.14   30.14   30.14   30.14  100.24  100.24  100.24

ELEM:       Ca       P       S      Al      Fe      As      Ba       K   SUM 
    84  37.971  17.987   -.002   -.007    .013    .227    .025   -.003 100.606
    85  38.465  17.962   -.001   -.008   -.007    .011    .002   -.001  99.534
    86  38.991  17.616   -.018    .004    .012    .050    .034    .006 100.038

AVER:   38.476  17.855   -.007   -.004    .006    .096    .020    .001 100.059
SDEV:     .510    .207    .010    .007    .011    .115    .016    .005    .536
SERR:     .295    .120    .006    .004    .006    .067    .009    .003
%RSD:     1.33    1.16 -140.09 -191.57  189.72  120.09   80.55  586.21

PUBL:   38.481  17.843    n.a.    n.a.    n.a.    n.a.    n.a.    n.a. 100.000
%VAR:   (-.01)   (.07)     ---     ---     ---     ---     ---     ---
DIFF:   (-.01)   (.01)     ---     ---     ---     ---     ---     ---
STDS:      285     285     327     336     160     662     835     336

STKF:    .3562   .1623   .2238   .1336   .0637   .5068   .6946   .0401
STCT:    740.7  4652.6  1673.7  6266.2  1409.7   586.0  3117.7   564.0

UNKF:    .3562   .1623  -.0001   .0000   .0000   .0007   .0001   .0000
UNCT:    740.7  4652.4     -.5    -1.3     1.1      .8      .6      .1
UNBG:      6.6    12.8     3.6    31.0    26.3     8.6     5.7    10.0

ZCOR:   1.0803  1.1000  1.1606  1.3187  1.2139  1.3521  1.5926  1.0850
KRAW:   1.0000  1.0000  -.0003  -.0002   .0008   .0014   .0002   .0002
PKBG:   113.58  369.01     .89     .96    1.04    1.09    1.11    1.02
INT%:     ----    ----    ----    ----    ----    ----    ----    ----

TDI%:    1.107    .530    .000   -.701    .617    ----    ----    ----
DEV%:       .3      .2      .0     1.1     2.3    ----    ----    ----
TDIF:  LOG-LIN LOG-LIN LOG-LIN LOG-LIN LOG-LIN    ----    ----    ----
TDIT:    56.33   37.00   56.00   54.67   57.00    ----    ----    ----
TDII:     747.   4666.    2.80    29.7    27.9    ----    ----    ----
TDIL:     6.62    8.45    1.03    3.39    3.33    ----    ----    ----
 
ELEM:       Mn      Na      Sr       F      Sm      Nd      Cl       Y
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL
BGDS:      LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN
TIME:    30.00   30.00   30.00   30.00   30.00   30.00   20.00   30.00
BEAM:   100.24  100.24  100.24  100.24  100.24  100.24  100.24  100.24

ELEM:       Mn      Na      Sr       F      Sm      Nd      Cl       Y   SUM 
    84    .002   -.001    .001   -.044   -.018    .004   7.547   -.016 100.606
    85    .018    .003    .005   -.117    .010   -.005   6.302   -.003  99.534
    86    .009    .002    .017   -.126    .037    .007   6.542   -.011 100.038

AVER:     .010    .001    .008   -.096    .010    .002   6.797   -.010 100.059
SDEV:     .008    .002    .008    .045    .028    .006    .661    .007    .536
SERR:     .005    .001    .005    .026    .016    .004    .381    .004
%RSD:    83.76  194.83  107.46  -46.93  281.24  286.57    9.72  -65.92

PUBL:     n.a.    n.a.    n.a.    n.a.    n.a.    n.a.   6.808    n.a. 100.000
%VAR:      ---     ---     ---     ---     ---     ---  (-.16)     ---
DIFF:      ---     ---     ---     ---     ---     ---  (-.01)     ---
STDS:       25     336     251     835    1011    1009     285    1016

STKF:    .7307   .0742   .3872   .1996   .4847   .4796   .0601   .3980
STCT:   4313.6  1769.9  3829.9   577.4  1129.8  3359.2   730.7  1079.3

UNKF:    .0001   .0000   .0001  -.0002   .0001   .0000   .0600  -.0001
UNCT:       .5      .1      .6     -.6      .1      .1   729.5     -.2
UNBG:      5.3    10.1     6.1     1.8     3.9    10.1     8.3     2.5

ZCOR:   1.2419  2.0160  1.3687  4.8155  1.5658  1.5508  1.1324  1.3564
KRAW:    .0001   .0001   .0001  -.0010   .0001   .0000   .9982  -.0002
PKBG:     1.09    1.01    1.09     .67    1.04    1.01   89.12     .92
INT%:     ----    ----    ---- -110.96     .19    -.59     .00    ----
 
ELEM:       Eu      Gd      Mg      La      Ce      Si       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC
BGDS:      AVG     LIN     LIN     LIN     LIN     LIN
TIME:    30.00   30.00   30.00   30.00   30.00   20.00     ---
BEAM:   100.24  100.24  100.24  100.24  100.24  100.24     ---

ELEM:       Eu      Gd      Mg      La      Ce      Si       O   SUM 
    84    .015    .003    .032   -.015    .009    .008  36.868 100.606
    85    .015   -.006    .033   -.008   -.012    .005  36.868  99.534
    86    .002   -.019    .027   -.016    .000    .006  36.868 100.038

AVER:     .011   -.007    .031   -.013   -.001    .006  36.868 100.059
SDEV:     .008    .011    .003    .005    .010    .001    .000    .536
SERR:     .005    .006    .002    .003    .006    .001    .000
%RSD:    72.59 -158.52   10.40  -36.15-1391.88   24.61     .00

PUBL:     n.a.    n.a.    n.a.    n.a.    n.a.    n.a.  36.868 100.000
%VAR:      ---     ---     ---     ---     ---     ---     .00
DIFF:      ---     ---     ---     ---     ---     ---    .000
STDS:     1004    1005     160    1007    1001     160     ---

STKF:    .4897   .4890   .0789   .4694   .4676   .1626     ---
STCT:   1247.5  5000.7  3048.5 11847.3  3558.3  5668.3     ---

UNKF:    .0001   .0000   .0002  -.0001   .0000   .0001     ---
UNCT:       .2     -.4     7.9    -2.1      .0     1.9     ---
UNBG:      4.5    18.1    19.3    54.1    21.4     5.1     ---

ZCOR:   1.5781  1.6049  1.5052  1.5738  1.5597  1.1215     ---
KRAW:    .0001  -.0001   .0026  -.0002   .0000   .0003     ---
PKBG:     1.04     .98    1.41     .96    1.00    1.37     ---
INT%:    -2.09   -5.66    ----     .18  -46.55    ----     ---

Of course most of the elements are labeled as n.a. for "not analyzed" because I haven't sacrificed any standard material for ICP-MS (I should do that!), but since it's a synthetic I might be able to assume that the starting materials were relatively pure for most contaminants.

So ignoring the Ca, P and Cl channels (which this is the primary standard for), the other trace elements (with the exception of Mg which is probably an uncorrected overlap from 3rd order Ca K), generally look to be within 1 or 2 standard deviations from zero, so this would give us some confidence that one can measure zero in this matrix for the other trace elements.

One could do the same for a very different matrix such as the NIST K-412 glass (which was the standard for Si, Al and Fe so ignore those channels in this case):

St  160 Set   3 NBS K-412 mineral glass, Results in Oxide Weight Percents

ELEM:      CaO    P2O5     SO3   Al2O3     FeO   As2O3     BaO     K2O   SUM 
   205  15.202    .044   -.023   9.442  10.049    .184   -.045    .004 100.427
   206  14.389    .019   -.032   9.253   9.960    .162   -.003    .014  99.458
   207  14.711    .000    .056   9.364   9.861    .203    .004    .008  99.941

AVER:   14.768    .021    .000   9.353   9.957    .183   -.015    .008  99.942
SDEV:     .410    .022    .048    .095    .094    .021    .027    .005    .484
SERR:     .236    .013    .028    .055    .054    .012    .015    .003
%RSD:     2.77  102.96    ----    1.01     .95   11.29 -181.99   59.43

PUBL:   15.250    n.a.    n.a.   9.270   9.960    n.a.    n.a.    n.a. 100.120
%VAR:    -3.16     ---     ---     .90  (-.04)     ---     ---     ---
DIFF:    -.482     ---     ---    .083   (.00)     ---     ---     ---
STDS:      285     285     327     336     160     662     835     336

ELEM:      MnO    Na2O     SrO       F   Sm2O3   Nd2O3      Cl    Y2O3   SUM 
   205    .091    .081    .042    .024    .017   -.007   -.004   -.002 100.427
   206    .094    .067    .049   -.024    .000   -.009    .006   -.009  99.458
   207    .090    .058    .060   -.005   -.026   -.007    .005   -.017  99.941

AVER:     .092    .069    .050   -.002   -.003   -.007    .002   -.009  99.942
SDEV:     .002    .012    .009    .024    .022    .001    .005    .008    .484
SERR:     .001    .007    .005    .014    .012    .001    .003    .004
%RSD:     2.21   17.25   17.21-1404.69 -763.06  -14.53  220.79  -81.53

PUBL:     .099    .058    n.a.    n.a.    n.a.    n.a.    n.a.    n.a. 100.120
%VAR:    -7.97   18.58     ---     ---     ---     ---     ---     ---
DIFF:    -.008    .011     ---     ---     ---     ---     ---     ---
STDS:       25     336     251     835    1011    1009     285    1016

ELEM:    Eu2O3   Gd2O3     MgO   La2O3   Ce2O3    SiO2       O   SUM 
   205   -.030    .007  19.333   -.016   -.026  45.269    .791 100.427
   206    .035    .006  19.291   -.021   -.029  45.432    .809  99.458
   207    .019   -.017  19.283   -.003    .003  45.490    .801  99.941

AVER:     .008   -.001  19.302   -.013   -.017  45.397    .800  99.942
SDEV:     .034    .014    .027    .009    .018    .115    .009    .484
SERR:     .019    .008    .016    .005    .010    .066    .005
%RSD:   416.32-1044.43     .14  -67.81 -102.03     .25    1.13

PUBL:     n.a.    n.a.  19.331    n.a.    n.a.  45.352    .800 100.120
%VAR:      ---     ---  (-.15)     ---     ---   (.10)     .02
DIFF:      ---     ---  (-.03)     ---     ---   (.04)    .000
STDS:     1004    1005     160    1007    1001     160     ---

Note that Na appears to be non-zero in the NIST glass but it is not reported, so the PUBL: value there is my own best attempt to quantify Na in K-412.  But the other elements again are all statistically within zero, with the possible exception of As and Sr. The Sr could be an uncorrected interference from Si Kb'.  Note sure what is going on with As. Has any one ever done a sensitive bulk technique on traces in the NIST K-412, K-411 glasses?

Anyway, something like this might be worth trying if you don't have an amphibole zero blank standard for traces.

Edit by John: just noticed that Mn is also statistically above zero in the K-412 glass. I've remember now that I've seen that  trace Mn for years.  Probably a contaminant.  One thing we could all use is more characterization of the trace elements in our standards...
3
Out of interest, does knowing that you can measure zero well, ensure you can accurately measure a well-characterized (with multiple techniques) CRM trace element glass like NIST 610? Have you tested it?

Hi Deon,
Having a zero (and matrix matched) zero blank ensures that one can measure accurately at the trace level.  See the earlier paper for more info:

http://epmalab.uoregon.edu/pdfs/3631Donovan.pdf

By having such a zero blank (and utilizing it in a blank correction) one now knows that their accuracy is equal to their measurement precision in that matrix for those elements. How nice is that!

I've looked at SRM 610 and 612 years ago and found them not to be very homogeneous. First of all note that they were never intended to used as microanalytical standards. Only for bulk methods. And even there it's problematic. For example the Mn value is 457 PPM +/- 55 PPM which means that one doesn't know whether the value is 400 PPM or 450 PPM or 500 PPM.  A range of 100 PPM is a lot of imprecision to have confidence in one's accuracy. 

Having a zero blank of that matrix glass would be far better in my opinion, as then one could know how well they can measure zero in that matrix with an accuracy equal to EPMA precision which could be only a few PPM for many elements.

In my original question, what I'm really asking, is if anyone out there routinely uses glass trace element standards successfully as secondary standards in the absence of availability of a  "zero blank" or a matrix-matched secondary standard.

I guess it depends on how one defines "successfully".   How would one know if they have been successful? 

What I would do is find a zero blank standard with a matrix as close as possible to the unknown in question, and utilize that in my blank correction in Probe for EPMA.  As I said before, extrapolating the matrix correction is accurate to a few percent or better. That is much better than the 10, 20 or 30% accuracy variance in the SRM trace values.  For oxide matrices even just a pure SiO2 synthetic glass would be more than close enough.  Again, the idea is to know that the chosen background positions, sample/detector absorption edges and spectral overlaps are being dealt with properly.

Here are some other topics on trace elements:

http://probesoftware.com/smf/index.php?topic=980.0

http://probesoftware.com/smf/index.php?topic=204.0

And here is a topic discussing using synthetic SiO2 as a blank standard:

http://probesoftware.com/smf/index.php?topic=130.0

Did I answer your question?  In your original post you mentioned trying to measure trace elements in amphibole. That's a tough material because it has so many elements and there are some spectral interferences, e.g., Mn Kb on Fe, Fe L on F Ka, etc..  Note that nasty as monazite but still tough when one wants to get accuracy below 100 PPM.

As I mentioned the NIST glass isn't certified for microanalysis (that I know of). In fact it's no longer available from NIST but it can still be purchased.  So it might be the next best thing for a secondary standard, but I'd also throw a synthetic SiO2 secondary standard in there because they are cheap and easily obtained.  After that I might look for a material such as a simple (synthetic?) silicate that has been measured for trace elements by more sensitive bulk techniques such as ICP-MS.

This post is getting long so I'm going to post another approach for you to consider next.
4
Hi John,

Out of interest, does knowing that you can measure zero well, ensure you can accurately measure a well-characterized (with multiple techniques) CRM trace element glass like NIST 610? Have you tested it?

In my original question, what I'm really asking, is if anyone out there routinely uses glass trace element standards successfully as secondary standards in the absence of availability of a  "zero blank" or a matrix-matched secondary standard.

Cheers,
Deon.
5
Perhaps this question needs to be a separate thread, but it's sort of relevant to the topic...

Does anyone analyze trace element glasses (SRMs) as secondary standards to check primary trace element calibrations that are intended for analysis of non-glass phases? E.g., say, analyzing a NIST glass with a routine intended for amphibole.

If so, do you find these glass analyses to be sufficiently accurate given the matrix differences between glass and primary standards?

Do you find that the beam diameter/current issues that affects major/minor element migration and signal variation in glasses also affect the accuracy of the traces?

Thanks,
Deon.

Hi Deon,
Lots to consider here. 

First remember that the accuracy of our modern matrix corrections are on the order of a few percent (and usually much better). If your precision trace element precision is better than that, well, good on you!   :)

In other words the difference in matrix will generally not be an issue for trace elements (in standards). We usually just want to use a primary standard with a high concentration of the elements and, as I've said before, a good secondary *blank* standard. Because the problem with non-zero trace element standards is their accuracy.  How are these non-zero values actually determined?  And how accurate is that technique?   

The most accurate trace element measurement we can make is usually a zero blank measurement where the element in question is *below* EPMA detection limits, so we get to see how well we can measure *zero* with an accuracy equal to our measurement precision.  In making a blank measurement it is best to have a matrix match, not because of the matrix correction accuracy, but because then we can know that we are properly handling all the other problems such as background positions, absorption edges and spectral interferences.

The two posts above lay out my thoughts on the matter.

On the question of beam sensitive samples for trace elements, yes, this can be a significant issue. Here is a discussion on trace elements started by Julien Allaz:

http://probesoftware.com/smf/index.php?topic=186.0

Note the TDI plots of U and Th attached at the bottom of his post.
john
6
PictureSnapApp (NEW!) / Re: PictureSnapApp version 1.6.6
« Last post by John Donovan on July 17, 2018, 05:47:54 pm »
The latest version of PictureSnapApp (v. 1.6.6) fixes the problem (on some systems) of "blinking" graphics. 

Download the app here:

http://probesoftware.com/download/PictureSnapApp.msi

Or simply use the Help | Update PictureSnapApp menu if you have it already installed on your computer. If you have any questions about this "visual notebook" application, please let us know.
7
Discussion of General EPMA Issues / IP address for JEOL probe and camera
« Last post by smontross on July 17, 2018, 04:33:14 pm »
Greetings,
We have a JEOL 8530 F Plus Hyperprobe and I am trying to figure out how to locate the IP address in order to set up communications with our network. The camera is functioning in stand alone mode, however, we are having issues getting it to communicate on our network. I will need these addresses in order for us to eventually set up the instrument for Team Viewer (remote) functioning.

Our IT tech staff has asked me to provide them with two IP addresses; 1) The actual JEOL IP address and the IP address for the camera. The IP addresses I need are not the same ones that I can recall with the Windows Command Prompt while the JEOL software is open.

Any idea would be greatly appreciated.

Scott Montross
8
General EDS Issues / Re: Missing peaks from thin film
« Last post by Probeman on July 17, 2018, 08:56:22 am »
Thanks Probeman,

Under the Analytical menu in Standard, the lower three entries including PENEPMA are greyed out. Is there another way of accessing the PENEPMA GUI?

Hi Dave,
Simply open any standard database using the File | Open menu. Penepma needs compositions to calculate spectra...

You can use the default standard database (standard.mdb) or a standard database of your own devising.
john
9
General EDS Issues / Re: Missing peaks from thin film
« Last post by Farqhuit on July 17, 2018, 08:53:09 am »
Thanks Probeman,

Under the Analytical menu in Standard, the lower three entries including PENEPMA are greyed out. Is there another way of accessing the PENEPMA GUI?

Cheers,

Dave
10
Probe for EPMA / Re: Questions about MAN background use
« Last post by Probeman on July 17, 2018, 08:29:47 am »
Hi John,
Both plots are correct.  But it is a little unintuitive, so good question!

The plotted (absorption corrected) MAN intensities in the Assign MAN Fits dialog are the "ideal" background intensities. They cannot be compared to actual measurements.  But by turning off the absorption correction in the MAN dialog, you are seeing the raw measured values, however which cannot be fitted together, because each MAN standard has different matrix physics.   But if the unknown matrix is the same as an individual MAN standard, then you can compare this "raw" intensity to off-peak measurements, as you observed. Please re-read the Donovan, et al. 2016 paper in Amer. Min for a complete explanation:

http://epmalab.uoregon.edu/publ/A%20new%20EPMA%20method%20for%20fast%20trace%20element%20analysis%20in%20simple%20matrices.pdf

In short, this is because each MAN standard is a different matrix and therefore needs to be corrected for the specific emission line individually before fitting.  Then once we have the equation of fit for these "ideal" intensities for the MAN standards, we can apply that fit to an actual sample after it is "de-corrected" for the actual absorption in the sample.

If you want to compare the calculated MAN background intensity with off-peak measurements, see the procedure here:

http://probesoftware.com/smf/index.php?topic=4.msg189#msg189

Then compare the line in the output labeled "UNBG:". Which are the MAN *or* off-peak intensities for the sample.
john
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