Author Topic: Using CalcZAF To Teach EPMA  (Read 15813 times)

Probeman

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Using CalcZAF To Teach EPMA
« on: April 09, 2014, 03:59:39 PM »
CalcZAF is a free EPMA utility program that can be downloaded here:

http://www.probesoftware.com/Technical.html

For a basic introduction to CalcZAF, please see this topic:

http://probesoftware.com/smf/index.php?topic=81.0

Here we will discuss using CalcZAF to teach EPMA physics. To begin with let's start with a very simple but significant system, e.g., Mg Ka absorbed by Fe. As one might imagine this matrix correction is important in most olivine and garnet analyses. A typical example from the default standard database will suffice by clicking the Enter Composition From database as seen here:



We can select any material containing both Mg and Fe, say this USNM olivine as seen here:



The application loads the composition as seen here:



and by clicking the Calculate button we obtain these results as seen here:



Now let's examine the results output to the log window  as seen here:

ELEMENT  ABSCOR  FLUCOR  ZEDCOR  ZAFCOR STP-POW BKS-COR   F(x)u      Ec   Eo/Ec    MACs
   Si ka  1.3766   .9998  1.0100  1.3901  1.0245   .9859   .6579  1.8390  8.1566 1561.39
   Fe ka   .9976  1.0000  1.1787  1.1758  1.2472   .9451   .9870  7.1120  2.1091 60.1050
   Mg ka  1.4944   .9963  1.0046  1.4958  1.0037  1.0009   .5798  1.3050 11.4943 2031.12
   Mn ka   .9993  1.0000  1.1952  1.1944  1.2655   .9444   .9834  6.5390  2.2939 74.0349
   Cr ka  1.0025   .9496  1.1685  1.1123  1.2370   .9446   .9775  5.9900  2.5042 97.3352
   O  ka  1.8671   .9988   .9485  1.7688   .9234  1.0272   .3753   .5317 28.2114 3874.87

 ELEMENT   K-RAW K-VALUE ELEMWT% OXIDWT% ATOMIC% FORMULA KILOVOL
   Si ka  .00000  .13097  18.207  38.951  14.157    .330   15.00
   Fe ka  .00000  .10987  12.919  16.620   5.052    .118   15.00
   Mg ka  .00000  .17570  26.281  43.582  23.615    .550   15.00
   Mn ka  .00000  .00194    .232    .300    .092    .002   15.00
   Cr ka  .00000  .00013    .014    .020    .006    .000   15.00
   O                      41.817    .000  57.078   1.330
   TOTAL:                 99.470  99.470 100.000   2.330


The column labeled "K-VALUE" is the calculated elemental k-ratio for the elements in question. That is, the intensity relative to a theoretical pure element. This can be compared to the element concentration (1.0 = 100%) to calculate the matrix correction factor. So for Mg Ka at 15 keV we have 0.1757 for the k-ratio intensity and 0.26281 for the concentration (26.281 wt.%). So 0.26282 / 0.1757 yields a correction factor of 1.49 or approximately 150%. A large absorption correction clearly which can be checked by looking at the ZAFCOR value for Mg.

Now of course this is only the case for the default physics model and that can be changed from the Analytical | ZAF, Phi-Rho-Z, Alpha factor and Calibration Curve Selections menu as seen here:



We can change the physics model by clicking the Options button and change the default mass absorption coefficient table by clicking the MACs button as seen here:



Let's select the traditional Heinrich MACs which are normally used by many programs and recalculate our k-ratios as seen here:

ELEMENT  ABSCOR  FLUCOR  ZEDCOR  ZAFCOR STP-POW BKS-COR   F(x)u      Ec   Eo/Ec    MACs
   Si ka  1.3762   .9998  1.0100  1.3898  1.0245   .9859   .6622  1.8390  8.1566 1534.50
   Fe ka   .9967  1.0000  1.1787  1.1748  1.2472   .9451   .9872  7.1120  2.1091 58.7753
   Mg ka  1.5252   .9964  1.0046  1.5267  1.0037  1.0009   .5720  1.3050 11.4943 2089.25
   Mn ka   .9978  1.0000  1.1952  1.1926  1.2655   .9444   .9834  6.5390  2.2939 73.7896
   Cr ka  1.0005   .9443  1.1685  1.1040  1.2370   .9446   .9783  5.9900  2.5042 93.5583
   O  ka  1.9086   .9988   .9485  1.8081   .9234  1.0272   .3672   .5317 28.2114 3987.35

 ELEMENT   K-RAW K-VALUE ELEMWT% OXIDWT% ATOMIC% FORMULA KILOVOL
   Si ka  .00000  .13101  18.207  38.951  14.157    .330   15.00
   Fe ka  .00000  .10997  12.919  16.620   5.052    .118   15.00
   Mg ka  .00000  .17214  26.281  43.582  23.615    .550   15.00
   Mn ka  .00000  .00195    .232    .300    .092    .002   15.00
   Cr ka  .00000  .00013    .014    .020    .006    .000   15.00
   O                      41.817    .000  57.078   1.330
   TOTAL:                 99.470  99.470 100.000   2.330


Note that the Mg Ka k-ratio went from 0.1757 to 1.7214 which is a change in the matrix correction from 1.49 to 1.52. Why would this matter to us? Well if the physics model overcalculates the matrix correction for Mg ka in Fe, we might get high totals.

In fact this is exactly the reason why so many researchers continue to get high totals for olivines and garnets. The Heinrich value is an interpolated value from the 1960's, the Henke value (the first calculation) is from the 1980s and here is the same calculation using the latest FFAST MACs:

ELEMENT  ABSCOR  FLUCOR  ZEDCOR  ZAFCOR STP-POW BKS-COR   F(x)u      Ec   Eo/Ec    MACs
   Si ka  1.3568   .9998  1.0100  1.3702  1.0245   .9859   .6726  1.8390  8.1566 1470.60
   Fe ka   .9981  1.0000  1.1787  1.1765  1.2472   .9451   .9874  7.1120  2.1091 58.0434
   Mg ka  1.4756   .9963  1.0046  1.4770  1.0037  1.0009   .5943  1.3050 11.4943 1926.57
   Mn ka  1.0000  1.0000  1.1952  1.1952  1.2655   .9444   .9835  6.5390  2.2939 73.4842
   Cr ka  1.0029   .9479  1.1685  1.1108  1.2370   .9446   .9782  5.9900  2.5042 93.9209
   O  ka  1.7590   .9988   .9485  1.6663   .9234  1.0272   .4072   .5317 28.2114 3470.77

 ELEMENT   K-RAW K-VALUE ELEMWT% OXIDWT% ATOMIC% FORMULA KILOVOL
   Si ka  .00000  .13288  18.207  38.951  14.157    .330   15.00
   Fe ka  .00000  .10981  12.919  16.620   5.052    .118   15.00
   Mg ka  .00000 .17794  26.281  43.582  23.615    .550   15.00
   Mn ka  .00000  .00194    .232    .300    .092    .002   15.00
   Cr ka  .00000  .00013    .014    .020    .006    .000   15.00
   O                      41.817    .000  57.078   1.330
   TOTAL:                 99.470  99.470 100.000   2.330


Note that using the most recently tabulated FFAST mass absorption coefficients, we now have a matrix correction of 1.475. A significantly different matrix correction, so yes, do not assume that your default MACs are "good enough"!

As a final (for now!) example, we can use the Analytical | Calculate and Plot Binary Alpha Factors menu as seen here where we have selected the Mg Ka in Fe matrix display:



Now you might ask: why is the displayed Y axis alpha factors showing around 2.5 instead of around 1.5?  It is the nature of alpha factors. Around 2.5 is the correction for Mg in Fe, but there is also the correction of Mg in Mg, which by definition is 1.0. So when we weight the contribution from each binary (Mg in Fe and Mg in Mg) we obtain a "beta-factor" of around 1.5 as seen here:

St  474 St  474 Olivine USNM 2566 (Fo 83) Springwater
TakeOff = 40.0  KiloVolt = 15.0  Density =  3.300

Analysis (wet chemistry) by Gene Jarosewich
Standard Z-bar:  12.53479

ELEM:       Si      Fe      Mg      Mn      Cr       O
ELWT:   18.207  12.919  26.281    .232    .014  41.817
NRWT:   18.207  12.919  26.281    .232    .014  41.817
BETA:   1.3679  1.1748  1.4819  1.1942  1.1403  1.7009
« Last Edit: May 22, 2015, 12:24:21 PM by John Donovan »
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John Donovan

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Re: Using CalcZAF To Teach EPMA
« Reply #1 on: May 22, 2015, 12:53:51 PM »
I recently implemented a new regression method for alpha factor matrix corrections as described here:

http://probesoftware.com/smf/index.php?topic=40.msg2762#msg2762

This new regression method improves the accuracy for situations in which very large fluorescence or absorption effects are present. This method can also be abused in situations in which some noise is present, for example low precision (low overvoltage or low concentration) Monte-Carlo derived k-ratios.

But first a short history of these regression efforts to model electron-solid interactions for binary pairs of elements over time as seen in this graphic:



The original method was proposed by Bob Ogilvie and others at MIT and applied to geological samples at Cal Tech (Bence and Albee) in the early 70's was to allow empirically measured k-ratios in binary compositions of known standards to be utilized for matrix corrections for complex materials. The Cal Tech implementation was originally based on assuming that the matrix correction did not vary as a function of the binary compositional range to facilitate the use of slide rules for calculations and therefore assumed the matrix correction at a 50:50 constant composition applied to all compositions for that binary.

This is not as crazy an assumption as one might think, for there are some binaries in which the matrix corrections are relatively constant over the binary range, for example as seen here:



Furthermore, for silicate matrices, which was the target main effort to improve matrix correct accuracy at Cal Tech, the matrix is mostly oxygen and therefore the matrix corrections were relatively more constant than in other systems.

However, it was soon realized by Mark Rivers (in the late 70's), then at UC Berkeley, that by rearranging the traditional alpha expression to solve for alpha, one could perform almost any regression equation to the alpha factor calculations. He applied a linear assumption which is far better than the constant assumption as seen here for the same dataset:



This was an enormous improvement in accuracy especially in non-geological matrices such as sulfides and other minerals and alloys.

But for instances where significant absorption or fluorescence effects are present John Armstrong in the late 80's (then at Cal Tech), noted that a polynomial fit would handle even these situations quite well as seen here for the famous Fe Ni binary:



Further details on the Rivers linear and Armstrong polynomial alpha factor methods can be found here:

http://epmalab.uoregon.edu/bence.htm

However, the keen eye will will notice that the polynomial fit isn't perfect and with the addition of a four coefficient non-linear regression even these extreme situations are dealt with properly as seen here for the same system:



Note that the average deviation for this non-linear expression is significantly improved, compared to the polynomial basis. For the record, the polynomial regression basis for the Mark Rivers alpha expression, (C/K - C)/(1 - C), is seen here:

alpha = coeff1 + conc * coeff2 + conc ^ 2 * coeff3

The corresponding beta expression (for summing binary alpha factors for complex matrices) for the polynomial fit is seen here:

beta = (coeff1 + conc * coeff2 + conc ^ 2 * coeff3) * conc

The regression basis for this new non-linear four coefficient fit is seen in the alpha expression here:

alpha = coeff1 + conc * coeff2 + conc ^ 2 * coeff3 + Exp(conc) * coeff4

and the corresponding beta expression for the non-linear fit is seen here:

beta = (coeff1 + conc * coeff2 + conc ^ 2 * coeff3 + Exp(conc) * coeff4) * conc

Remember: all this fitting takes place in hyperbolic space due to the nature of the alpha concentration - kratio relationship as first described by Ogilvie!
« Last Edit: December 21, 2015, 11:14:19 AM by John Donovan »
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Re: Using CalcZAF To Teach EPMA
« Reply #2 on: May 22, 2015, 01:00:47 PM »
And even for extreme absorption situations, this non-linear alpha expression shows improved accuracy as seen for the fluorine - oxygen system, first here as a polynomial fit:



and here the same system with a non-linear regression:

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Re: Using CalcZAF To Teach EPMA
« Reply #3 on: May 22, 2015, 03:01:10 PM »
Now some of you might ask: what is the point of all these complex alpha calculations? After all, weren't they originally invented because the physics of ZAF matrix corrections were quite inaccurate at that time in the early 1970's?

Yes, it is true that one of the original rationales for implementing the alpha matrix correction method was because one could utilize empirically measured k-ratios for what amounts to a hyperbolic calibration curve. But there are two other benefits to alpha factors, first for quantitative imaging. The example here is a small (5 elements, 128x128 pixel) map, but an 11 percent improvement is an 11% improvement!

Here is a speed comparison for a small mapping project:

JTA-Reed Phi-Rho-Z:   4 min: 29 sec
Single Term Alpha:   4 min: 04 sec
Two Term Alpha:   4 min: 12 sec
Three Term Alpha:   4 min: 02 sec
Four Term Alpha:   4 min: 04 sec

Of course the real speed (and accuracy) benefit will come from fitting Monte-Carlo derived k-ratios for alpha factor corrections. The idea being to obtain Monte-Carlo physics rigor in seconds instead of days or months!  See here for more details:

http://probesoftware.com/smf/index.php?topic=152.0
« Last Edit: May 23, 2015, 02:47:47 PM by John Donovan »
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smatveev

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Re: Using CalcZAF To Teach EPMA
« Reply #4 on: July 14, 2015, 09:23:36 AM »
Dear John,
First of all let me thank you for making  such excellent invaluable tool as CalcZAF available for everyone to use for teaching and modelling. 

Regarding example of olivine calculation given above, it interestingly resonates with one of the recent cases in our laboratory. Our laboratory is equipped with JEOL 8530F. We have ambitious customer requesting high quality olivine analysis for both major and trace elements. In the first part of the procedure we measure 3 elements Fe, Mg and Si at regular conditions 15kV and 20 nA. All elements are calibrated using San Carlos olivine USNM 111312-44. Later the same grain is used as secondary standard. However analytical  results were not accepted as Mg concentrations were systematically lower than tabulated value even though k-raw values were all close to or slightly higher than 1. We used CalcZAF to test different corrections and found that Bastin PROZA and XPP with FFAST MACs  produce better result. However we failed to fully reproduce the standard even assuming k-raw values unity. No matter how hard we tried, Mg values were pushed down by correction procedures.

The SCOlivine setup was as follows:


Elemental Weight Percents:
ELEM:       Si      Mg      Fe       O   TOTAL
     1  19.062  29.698   7.437  43.400  99.597   Armstrong/Love Scott (default)
     2  19.067  29.703   7.437  43.409  99.616   Conventional Philibert/Duncumb-Reed
     3  19.064  29.696   7.436  43.400  99.595   Heinrich/Duncumb-Reed
     4  19.064  29.700   7.437  43.403  99.605   Love-Scott I
     5  19.063  29.699   7.437  43.402  99.601   Love-Scott II
     6  19.074  29.719   7.437  43.427  99.657   Packwood Phi(pz) (EPQ-91)
     7  19.066  29.700   7.437  43.406  99.609   Bastin (original) Phi(pz)
     8  19.067  29.718   7.438  43.418  99.640   Bastin PROZA Phi(pz) (EPQ-91)
     9  19.067  29.701   7.437  43.407  99.612   Pouchou and Pichoir-Full (Original)
    10  19.067  29.704   7.437  43.410  99.618   Pouchou and Pichoir-Simplified (XPP)

As seen from the calculation results Mg values are systematically below the standard value 29.80wt%. When recalculated to oxides the difference becomes more depressing to the customer. We explain how corrections have to be applied and that is how we can use standards different from unknown. At this point customer gets out a bunch of publications, where stated mean measured value is practically identical to the standard value. The question is: is there a way other than MS Excel "correction" to obtain accurate Mg values in forsteritic olivine using currently available matrix corrections?
Best regards,
Sergei Matveev
« Last Edit: July 14, 2015, 10:48:02 AM by John Donovan »

Probeman

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Re: Using CalcZAF To Teach EPMA
« Reply #5 on: July 14, 2015, 11:30:07 AM »
Regarding example of olivine calculation given above, it interestingly resonates with one of the recent cases in our laboratory. Our laboratory is equipped with JEOL 8530F. We have ambitious customer requesting high quality olivine analysis for both major and trace elements. In the first part of the procedure we measure 3 elements Fe, Mg and Si at regular conditions 15kV and 20 nA. All elements are calibrated using San Carlos olivine USNM 111312-44. Later the same grain is used as secondary standard. However analytical  results were not accepted as Mg concentrations were systematically lower than tabulated value even though k-raw values were all close to or slightly higher than 1. We used CalcZAF to test different corrections and found that Bastin PROZA and XPP with FFAST MACs  produce better result. However we failed to fully reproduce the standard even assuming k-raw values unity. No matter how hard we tried, Mg values were pushed down by correction procedures.

As seen from the calculation results Mg values are systematically below the standard value 29.80wt%. When recalculated to oxides the difference becomes more depressing to the customer. We explain how corrections have to be applied and that is how we can use standards different from unknown. At this point customer gets out a bunch of publications, where stated mean measured value is practically identical to the standard value. The question is: is there a way other than MS Excel "correction" to obtain accurate Mg values in forsteritic olivine using currently available matrix corrections?
Best regards,
Sergei Matveev

Hi Sergei,
I want to make sure I understand your problem, but first of all: thank-you.

You are saying that if you analyze the San Carlos olivine as a secondary standard and also use the *same* San Carlos olivine grain as the primary standard, you get low values for Mg?  That doesn't sound good.

Here are some speculations:

1. How old is the San Carlos olivine (primary) standard calibration?  Maybe it needs to be re-calibrated due to detector drift?

2. Are you sure you utilized the same grain for both the secondary and primary standard measurements?  San Carlos olivine is not really a standard. At least many of what people call San Carlos olivine is not really from the Smithsonian, just from the locality.  Please note that it has been shown that San Carlos olivine is quite variable, even within a single grain. I believe John Fournelle showed this at an M&M talk some time ago...

3. I think you would be much better off utilizing MgO or synthetic Mg2SiO4 as a Mg standard. In fact synthesizing Mg2SiO4 is one of our crowd sourcing efforts as described here:

http://probesoftware.com/smf/index.php?topic=301.0

I happen to have a beautiful chunk of single crystal Mg2SiO4 I got many years ago from the Institute of Solid State Physics in Japan and use it all the time.  Perfectly stoichiometric and provides an excellent primary standard.  If I run it against MgO I always get something like this:

St  273 Set   1 Mg2SiO4 (magnesium olivine) synthetic, Results in Elemental Weight Percents
 
ELEM:       Si      Al      Fe      Mg      Cr      Ti      Mn      Ca       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC
BGDS:      LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN
TIME:    20.00   20.00   20.00   20.00   20.00   20.00   20.00   20.00     ---
BEAM:    20.08   20.08   20.08   20.08   20.08   20.08   20.08   20.08     ---

ELEM:       Si      Al      Fe      Mg      Cr      Ti      Mn      Ca       O   SUM 
   136  19.960    .006    .040  34.696   -.007   -.020    .008    .000  45.486 100.170
   137  19.957   -.011   -.022  34.840   -.013    .000    .033    .009  45.486 100.279
   138  19.904    .004    .024  34.684    .015    .000   -.007    .014  45.486 100.124
   139  19.951    .005    .013  34.723   -.004    .023   -.019    .005  45.486 100.183
   140  19.909   -.006   -.008  34.748   -.016    .042    .004    .013  45.486 100.173

AVER:   19.936   -.001    .010  34.738   -.005    .009    .004    .008  45.486 100.186
SDEV:     .027    .008    .025    .062    .012    .024    .019    .006    .000    .057
SERR:     .012    .003    .011    .028    .005    .011    .009    .003    .000
%RSD:      .14-1119.60  252.60     .18 -236.08  264.62  519.51   69.67     .00

PUBL:   19.960    n.a.    n.a.  34.554    n.a.    n.a.    n.a.    n.a.  45.486 100.000
%VAR:     -.12     ---     ---     .53     ---     ---     ---     ---     .00
DIFF:    -.024     ---     ---    .184     ---     ---     ---     ---    .000
STDS:       14      13     395      12      24      22      25     358     ---

STKF:    .4118   .4367   .6812   .4746   .6434   .5581   .7370   .1707     ---
STCT:  16416.0 17474.8  2687.8 20396.4  2037.4  1144.4  2745.9  2349.6     ---

UNKF:    .1424   .0000   .0001   .2616   .0000   .0001   .0000   .0001     ---
UNCT:   5678.6     -.2      .3 11243.2     -.1      .2      .1     1.0     ---
UNBG:     26.0    16.5     3.9    18.2     2.2     1.2     3.0     9.1     ---

ZCOR:   1.3996  1.6862  1.1873  1.3279  1.1825  1.1821  1.2058  1.1003     ---
KRAW:    .3459   .0000   .0001   .5512  -.0001   .0001   .0000   .0004     ---
PKBG:   219.54    1.00    1.11  618.02     .96    1.20    1.05    1.12     ---


Note that extrapolating from MgO to Mg2SiO4 is within 0.5% relative accuracy! And this is a factor of two difference in intensity and a matrix correction of around 30%.

4. If you can't get the secondary standard and primary standard to agree you have a real problem. Especially if they are the same standard! You mentioned a FEG EPMA.  These instruments can focus a lot of beam into a very small volume and damage specimens that we used to consider "beam stable".  Did you run *exactly* the same analytical conditions and acquisition times on both the primary and secondary standard and the same grain?  This would be a good sanity check so I would start with that.

5. Aside from all that there is a very large absorption correction for Mg Ka by Fe. Here are some MACs from a number of tabulations (you can do this yourself in CalcZAF from the X-Ray menu):

MAC value for Mg ka in Fe =    5239.40  (LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV)
MAC value for Mg ka in Fe =    6120.70  (CITZMU   Heinrich (1966) and Henke and Ebisu (1974))
MAC value for Mg ka in Fe =    5395.10  (MCMASTER McMaster (LLL, 1969) (modified by Rivers))
MAC value for Mg ka in Fe =    5518.65  (MAC30    Heinrich (Fit to Goldstein tables, 1987))
MAC value for Mg ka in Fe =    6089.53  (MACJTA   Armstrong (FRAME equations, 1992))
MAC value for Mg ka in Fe =    5089.56  (FFAST    Chantler (NIST v 2.1, 2005))
MAC value for Mg ka in Fe =    5089.56  (USERMAC  User Defined MAC Table)


So there is some significant disagreement in the fundamental physics.  I will only note that the Heinrich value which was and is still being used by many software packages, is anomalously high.  In fact, this is usually the problem when people report high totals in garnets, etc.  See here:

http://epmalab.uoregon.edu/UCB_EPMA/problems.htm

However, since you are using the same standard for both the primary and secondary standard, the MAC is irrelevant. Instead you have a fundamental measurement problem.  The k-ratio in this particular case *must* be 1.000.

This is what I say say for starters.
john
« Last Edit: July 15, 2015, 08:37:23 AM by Probeman »
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Probeman

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Re: Using CalcZAF To Teach EPMA
« Reply #6 on: July 14, 2015, 12:14:02 PM »
By the way, I also calculated the MgO (primary) to Mg2SiO4 (secondary) extrapolation here using all 10 different matrix corrections:

Summary of All Calculated (averaged) Matrix Corrections:
St  273 Set   1 Mg2SiO4 (magnesium olivine) synthetic
LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV

Elemental Weight Percents:
ELEM:       Si      Al      Fe      Mg      Cr      Ti      Mn      Ca       O   TOTAL
     1  19.940   -.001    .010  34.734   -.005    .009    .004    .008  45.486 100.185   Armstrong/Love Scott (default)
     2  20.332   -.001    .010  34.670   -.005    .009    .004    .008  45.486 100.514   Conventional Philibert/Duncumb-Reed
     3  20.221   -.001    .010  34.816   -.005    .009    .004    .008  45.486 100.547   Heinrich/Duncumb-Reed
     4  20.062   -.001    .010  34.757   -.005    .009    .004    .008  45.486 100.330   Love-Scott I
     5  19.934   -.001    .010  34.725   -.005    .009    .004    .008  45.486 100.170   Love-Scott II
     6  19.826   -.001    .010  34.627   -.005    .009    .004    .008  45.486  99.965   Packwood Phi(pz) (EPQ-91)
     7  20.162   -.001    .010  34.732   -.005    .009    .004    .008  45.486 100.405   Bastin (original) Phi(pz)
     8  19.405   -.001    .010  34.613   -.005    .009    .004    .008  45.486  99.529   Bastin PROZA Phi(pz) (EPQ-91)
     9  20.219   -.001    .010  34.797   -.005    .009    .004    .008  45.486 100.528   Pouchou and Pichoir-Full (Original)
    10  20.117   -.001    .010  34.753   -.005    .009    .004    .008  45.486 100.382   Pouchou and Pichoir-Simplified (XPP)

AVER:   20.022   -.001    .010  34.722   -.005    .009    .004    .008  45.486 100.255
SDEV:     .266    .000    .000    .067    .000    .000    .000    .000    .000    .315
SERR:     .084    .000    .000    .021    .000    .000    .000    .000    .000

MIN:    19.405   -.001    .010  34.613   -.005    .009    .004    .008  45.486  99.529
MAX:    20.332   -.001    .010  34.816   -.005    .009    .004    .008  45.486 100.547

This is using the Henke MAC value for Mg ka in Fe. The correct (stoichiometric) value for Mg in Mg2SiO4 should be 34.550. However, if I now select the most modern value tabulated for Mg Ka in Fe from the NIST FFAST table I get the following results:

Summary of All Calculated (averaged) Matrix Corrections:
St  273 Set   1 Mg2SiO4 (magnesium olivine) synthetic
FFAST    Chantler (NIST v 2.1, 2005)

Elemental Weight Percents:
ELEM:       Si      Al      Fe      Mg      Cr      Ti      Mn      Ca       O   TOTAL
     1  19.752   -.001    .010  34.668   -.005    .009    .004    .008  45.486  99.932   Armstrong/Love Scott (default)
     2  20.147   -.001    .010  34.606   -.005    .009    .004    .008  45.486 100.264   Conventional Philibert/Duncumb-Reed
     3  20.037   -.001    .010  34.753   -.005    .009    .004    .008  45.486 100.301   Heinrich/Duncumb-Reed
     4  19.864   -.001    .010  34.689   -.005    .009    .004    .008  45.486 100.064   Love-Scott I
     5  19.743   -.001    .010  34.657   -.005    .009    .004    .008  45.486  99.911   Love-Scott II
     6  19.646   -.001    .010  34.565   -.005    .009    .004    .008  45.486  99.723   Packwood Phi(pz) (EPQ-91)
     7  19.973   -.001    .010  34.668   -.005    .009    .004    .008  45.486 100.152   Bastin (original) Phi(pz)
     8  19.249   -.001    .010  34.555   -.005    .009    .004    .008  45.486  99.316   Bastin PROZA Phi(pz) (EPQ-91)
     9  20.017   -.001    .010  34.730   -.005    .009    .004    .008  45.486 100.258   Pouchou and Pichoir-Full (Original)
    10  19.926   -.001    .010  34.689   -.005    .009    .004    .008  45.486 100.127   Pouchou and Pichoir-Simplified (XPP)

AVER:   19.835   -.001    .010  34.658   -.005    .009    .004    .008  45.486 100.005
SDEV:     .257    .000    .000    .065    .000    .000    .000    .000    .000    .303
SERR:     .081    .000    .000    .021    .000    .000    .000    .000    .000

MIN:    19.249   -.001    .010  34.555   -.005    .009    .004    .008  45.486  99.316
MAX:    20.147   -.001    .010  34.753   -.005    .009    .004    .008  45.486 100.301


If I just take the default matrix correction (JTA phi-rho-z) I get this:

St  273 Set   1 Mg2SiO4 (magnesium olivine) synthetic, Results in Elemental Weight Percents
 
ELEM:       Si      Al      Fe      Mg      Cr      Ti      Mn      Ca       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC
BGDS:      LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN
TIME:    20.00   20.00   20.00   20.00   20.00   20.00   20.00   20.00     ---
BEAM:    20.08   20.08   20.08   20.08   20.08   20.08   20.08   20.08     ---

ELEM:       Si      Al      Fe      Mg      Cr      Ti      Mn      Ca       O   SUM 
   136  19.773    .006    .040  34.630   -.007   -.020    .008    .000  45.486  99.916
   137  19.769   -.011   -.022  34.774   -.013    .000    .033    .009  45.486 100.025
   138  19.717    .004    .024  34.618    .015    .000   -.007    .014  45.486  99.871
   139  19.764    .005    .013  34.657   -.004    .023   -.019    .005  45.486  99.930
   140  19.722   -.006   -.008  34.682   -.016    .042    .004    .013  45.486  99.919

AVER:   19.749   -.001    .010  34.672   -.005    .009    .004    .008  45.486  99.932
SDEV:     .027    .008    .025    .062    .012    .024    .019    .006    .000    .056
SERR:     .012    .003    .011    .028    .005    .011    .009    .003    .000
%RSD:      .14-1119.50  252.60     .18 -236.08  264.62  519.50   69.67     .00

PUBL:   19.960    n.a.    n.a.  34.554    n.a.    n.a.    n.a.    n.a.  45.486 100.000
%VAR:    -1.06     ---     ---     .34     ---     ---     ---     ---     .00
DIFF:    -.211     ---     ---    .118     ---     ---     ---     ---    .000
STDS:       14      13     395      12      24      22      25     358     ---

STKF:    .4138   .4404   .6811   .4790   .6433   .5578   .7369   .1706     ---
STCT:  16416.0 17474.8  2687.8 20396.4  2037.4  1144.4  2745.9  2349.6     ---

UNKF:    .1431   .0000   .0001   .2640   .0000   .0001   .0000   .0001     ---
UNCT:   5678.6     -.2      .3 11243.2     -.1      .2      .1     1.0     ---
UNBG:     26.0    16.5     3.9    18.2     2.2     1.2     3.0     9.1     ---

ZCOR:   1.3797  1.6799  1.1881  1.3131  1.1831  1.1834  1.2069  1.1002     ---
KRAW:    .3459   .0000   .0001   .5512  -.0001   .0001   .0000   .0004     ---
PKBG:   219.54    1.00    1.11  618.02     .96    1.20    1.05    1.12     ---


Now our relative accuracy error for Mg is 0.3%.  I would not complain too much about this result... though our Si value did get slightly worse compared to the Henke MAC table!   :'( 
« Last Edit: July 14, 2015, 12:16:46 PM by Probeman »
The only stupid question is the one not asked!

JohnF

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Re: Using CalcZAF To Teach EPMA
« Reply #7 on: July 14, 2015, 12:31:58 PM »
Sergei

Interesting question ... and opportunity to look at the 'black box' of the matrix correction.
 
-- you were using raw K-ratios of 1 or slightly greater than one for your CalcZAF calculations.

So I went and ran calczaf myself, for the published San Carlos composition which shows Mg as 29.80 wt %, using ONLY Si, Fe and Mg (and stoic oxygen) and I got the same low value for Mg (0.10 wt% low). Hmmm.
Note that I had loaded the proper composition using the Enter Composition from Database button, and then
chose the option Calculate Weight Concentrations from Intensities (K-raw), then selected each element, assigned the standard to be the SC olivine from my PfE database, and also entered Intensity (k-raw) as 1.000. Then calculated.
When ALL the elements including Ca, Mn and Ni are entered, calczaf does spit out 29.80 as the Mg wt%.
So I then went thru and deleted elements one by one.
Deleted Ca and Mg is now 29.797, not much change
Deleted Mn and Mg is now 29.781, decrease a bit
Deleted Ni and guess what, Mg is now 29.704...exactly the number you saw.

Thus, those small amounts of Ni cause a change in the matrix correction, enough to have Mg low by 1000 ppm or 0.1 wt%.

What John D was referring to  was the fact that non-Smithsonian San Carlos grains can be significantly different from the published USNM values. Also, as I have shown, there are slight variations in the USNM olivine and one really _should_ calibrate using 5-10 grains of it (and of all such small sized crystals distributed the the Smithsonian. (I am quoting Gene Jarosewich.)

Probeman

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Re: Using CalcZAF To Teach EPMA
« Reply #8 on: July 14, 2015, 01:15:19 PM »
Interesting question ... and opportunity to look at the 'black box' of the matrix correction.

Hi John,
By the way, CalcZAF will no longer be a "black box" after this summer when we open source it here:

https://groups.google.com/forum/#!forum/openmicroanalysis

Of course anyone can obtain the source code on request so it has never really been a true "black box".

When ALL the elements including Ca, Mn and Ni are entered, calczaf does spit out 29.80 as the Mg wt%.
So I then went thru and deleted elements one by one.
Deleted Ca and Mg is now 29.797, not much change
Deleted Mn and Mg is now 29.781, decrease a bit
Deleted Ni and guess what, Mg is now 29.704...exactly the number you saw.

Thus, those small amounts of Ni cause a change in the matrix correction, enough to have Mg low by 1000 ppm or 0.1 wt%.

Excellent detective work!  I never would have guessed that a trace amount of Ni could have that much effect on the Mg ka matrix correction! 

By the way, here are the MACs for Mg Ka by Ni

MAC value for Mg ka in Ni =    6506.00  (LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV)
MAC value for Mg ka in Ni =    7709.50  (CITZMU   Heinrich (1966) and Henke and Ebisu (1974))
MAC value for Mg ka in Ni =    6911.97  (MCMASTER McMaster (LLL, 1969) (modified by Rivers))
MAC value for Mg ka in Ni =    6856.25  (MAC30    Heinrich (Fit to Goldstein tables, 1987))
MAC value for Mg ka in Ni =    7657.83  (MACJTA   Armstrong (FRAME equations, 1992))
MAC value for Mg ka in Ni =    6327.90  (FFAST    Chantler (NIST v 2.1, 2005))
MAC value for Mg ka in Ni =    6327.90  (USERMAC  User Defined MAC Table)


Even worse than for Fe.
« Last Edit: July 15, 2015, 08:37:06 AM by Probeman »
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smatveev

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Re: Using CalcZAF To Teach EPMA
« Reply #9 on: July 15, 2015, 06:53:00 AM »
Dear John F and John D,
Thank you very much for fast and comprehensive answers!
Regarding conditions, very good point, we defocus beam to 1-3 micron diameter for regular WDS analysis. I keep it focused only for analysis of thin electron-transparent suspended films (no substrate), but such samples are much tougher than they look.... or the damage is confined to a small spot, less apparent ).
We performed analysis of SC olivine immediately after calibration and were planning to set up different protocol for trace element analysis (including Ni) at much harsher conditions (400nA). K-raw values were close to ideal, precision was excellent, but Mg was below the tabulated value. As I can see now we have greatly underestimated absorption of Mg Ka by Ni. I checked it with our data and when merged together, values are perfect. Thank you very much John F for figuring out dramatic effect of Ni on Mg values, thank you both for your help, greatly appreciated!
Sergei


Major Elements, no Ni

Unknown Specimen No. 54
 Path         : 10july2015      Project : quant_0008     
 Position No. :   54            Comment : SCOline1 Line 001
 Stage        :    X=  -26.0097  Y=    2.0290  Z=   10.5080
 Acc. Voltage :    15.0 (kV)    Probe Dia. : 1    Scan : Off
 Dated on 2015/07/10 19:47:18
 WDS only       No. of accumulation : 1

Curr.(A) : 2.001E-008
Element Peak(mm) Net(cps)   Bg-   Bg+  S.D.(%)   D.L.(ppm)  K-raw(%)   
 1 Si    77.450   7421.6   28.4   25.6    0.21       71     100.891
 2 Mg   107.532  11711.4   40.6   43.9    0.16       69     100.458
 3 Fe   134.805   1086.3   26.3   19.7    0.55      104      99.714


Element  f(chi)    If/Ip     abs-el    1/s-el      r-el      c/k-el    c/k-std
 Si      0.6645    0.0001    0.7323    0.9480     1.0186     1.4140     0.9993
 Mg      0.6195    0.0038    0.7115    0.9739     1.0050     1.4307     0.9963
 Fe      0.9856    0.0000    1.0026    0.7652     1.0630     1.2262     1.0019

Element  El. mass% Ox mass% Norm El%  Norm ox%  At prop  k-value   k-(std)
 Si      19.18     41.03     19.21     41.09     6.022   0.13565   1.00891 
 Mg      29.75     49.32     29.79     49.39    10.790   0.20788   1.00458 
 Fe       7.39      9.51      7.40      9.52     1.167   0.06028   0.99714 
 O       43.55       -       43.61       -      24.000      -         -       
 -----------------------------------------------------------------------------
Total:   99.87     99.87    100.00    100.00    17.978

Full analysis:

Unknown Specimen No. 54
 Path         :           Project : SCOLine1_0001 
 Position No. :   54            Comment : SCOline1 Line 001
 Stage        :    X=  -26.0097  Y=    2.0290  Z=   10.5080
 Acc. Voltage :    15.0  0.0 (kV)    Probe Dia. : 1    Scan : Off
 Dated on 2015/07/10 19:47:18
 WDS only       No. of accumulation : 1

Curr.(A) : 2.001E-008
Element Peak(mm) Net(cps)   Bg-   Bg+  S.D.(%)   D.L.(ppm)  Curr.(A)  Acc.V  K-raw(%)   
 1 Si    77.450   7421.6   28.4   25.6    0.08       29    2.001E-008   15.0     100.891
 2 Na   129.570     11.8  151.8   98.7    3.08        2    4.017E-007   15.0       0.040
 3 Cr    73.575     71.6 2350.0 1833.3    2.99        3    4.017E-007   15.0       0.008
 4 Ti    88.281      3.1 1272.5 1074.7   50.89 ?      3    4.017E-007   15.0       0.000
 5 P    197.240      2.3   65.9   59.3   13.07        2    4.017E-007   15.0       0.005
 6 Ca   107.495    755.2  939.3  714.4    0.30        2    4.017E-007   15.0       0.396
 7 Mg   107.532  11711.4   40.6   43.9    0.07       28    2.001E-008   15.0     100.458
 8 Al    90.772    100.2 1174.5  879.8    1.08        2    4.017E-007   15.0       0.019
 9 Fe   134.805   1086.3   26.3   19.7    0.22       43    2.001E-008   15.0      99.714
10 Mn   146.345    299.2  366.5  298.4    0.47        5    4.017E-007   15.0       0.191
11 Ni   115.437    812.4  747.4  625.3    0.19        5    4.017E-007   15.0       0.249
12 Co   124.565     65.2  627.5  529.3    2.45        6    4.017E-007   15.0       0.019


Element  f(chi)    If/Ip     abs-el    1/s-el      r-el      c/k-el    c/k-std
 Si      0.6638    0.0001    0.7316    0.9490     1.0182     1.4144     0.9996
 Cr      0.9752    0.0265    0.9970    0.7741     1.0616     1.1890     1.1890
 Ca      0.9232    0.0035    0.9599    0.8739     1.0506     1.1308     1.0098
 Mg      0.6167    0.0037    0.7083    0.9749     1.0046     1.4362     1.0002
 Al      0.5434    0.0066    0.6110    0.9337     1.0115     1.7216     1.3963
 Fe      0.9855    0.0012    1.0026    0.7660     1.0628     1.2238     1.0000
 Mn      0.9811    0.0008    1.0003    0.7558     1.0626     1.2437     1.1045
 Ni      0.9862    0.0000    0.9995    0.7708     1.0606     1.2238     1.2238
 Co      0.9888    0.0000    1.0039    0.7470     1.0621     1.2554     1.2554

Element  El. mass% Ox mass% Norm El%  Norm ox%  At prop  k-value   k-(std)
 Si      19.18     41.02     19.05     40.74     5.990   0.13565   1.00891 
 Na       0.0048    0.0065    0.0048    0.0064   0.0018   0.000026  0.000395 
 Cr       0.0089    0.0130    0.0089    0.0129   0.0015   0.000075  0.000075 
 Ti       0.0004    0.0007    0.0004    0.0007   0.0001   0.000004  0.000005 
 P        0.0010    0.0022    0.0010    0.0022   0.0003   0.000006  0.000047 
 Ca       0.0731    0.1023    0.0726    0.1016   0.0160   0.000647  0.003956 
 Mg        29.83   49.46     29.62     49.12    10.766   0.20788   1.00458 
 Al       0.0138    0.0261    0.0137    0.0259   0.0045   0.000080  0.000187 
 Fe       7.38      9.49      7.33      9.42     1.159   0.06028   0.99714 
 Mn       0.1149    0.1483    0.1141    0.1473   0.0183   0.000924  0.001912 
 Ni       0.3046    0.3876    0.3025    0.3849   0.0455   0.002489  0.002489 
 Co       0.0235    0.0299    0.0233    0.0296   0.0035   0.000187  0.000187 
 O       43.76       -       43.46       -      24.000      -         -       
 -----------------------------------------------------------------------------
Total:  100.69    100.69    100.00    100.00    18.007


« Last Edit: December 21, 2015, 11:19:42 AM by John Donovan »

Probeman

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    • John Donovan
Re: Using CalcZAF To Teach EPMA
« Reply #10 on: July 15, 2015, 07:58:16 AM »
We performed analysis of SC olivine immediately after calibration and were planning to set up different protocol for trace element analysis (including Ni) at much harsher conditions (400nA). K-raw values were close to ideal, precision was excellent, but Mg was below the tabulated value.

Hi Sergei,
Remember, when performing trace analyses it is better to check if one can measure a zero (or very small non zero) concentration in a similar matrix material.

Checking accuracy on a secondary major element standard is useful for major element accuracy checks, but for trace elements you want to be sure you can measure zero accurately because the background measurement becomes the dominant source of error!  Ideally for trace analysis, you should check if you can measure zero Ni on a pure synthetic Mg2SiO4 or Fe2SiO4 standard.

See here for more details:

http://probesoftware.com/smf/index.php?topic=29.msg387#msg387
« Last Edit: July 15, 2015, 08:36:49 AM by Probeman »
The only stupid question is the one not asked!

smatveev

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Re: Using CalcZAF To Teach EPMA
« Reply #11 on: July 15, 2015, 08:17:34 AM »
John, thank you, very good point! I will test our "blanks".
On slightly different aspect of trace element analysis. Our software manual states that (at least in case of ZAF correction): the calculation is iterated until the calculation error is reduced to within 0.001 mass% or until the tenth iteration. My question is, how other packages treat iteration process and how does it affect detection limits of quantitative analysis?
Sergei

Probeman

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Re: Using CalcZAF To Teach EPMA
« Reply #12 on: July 15, 2015, 08:36:07 AM »
John, thank you, very good point! I will test our "blanks".
On slightly different aspect of trace element analysis. Our software manual states that (at least in case of ZAF correction): the calculation is iterated until the calculation error is reduced to within 0.001 mass% or until the tenth iteration. My question is, how other packages treat iteration process and how does it affect detection limits of quantitative analysis?

Huh, that's a good question. I never thought about that limitation but I think you are correct that if your iteration only iterates to 10 PPM that might be a problem for ultra trace elements. 

Of course it would only be a problem if you are analyzing all trace elements, since if a major element is present in the iteration that will dominate the matrix correction loop...

I can only speak to my code which iterates until the changes are less than 1 PPM:  ZAF_Min_Toler! = 0.0001
« Last Edit: July 15, 2015, 09:21:30 AM by John Donovan »
The only stupid question is the one not asked!

smatveev

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Re: Using CalcZAF To Teach EPMA
« Reply #13 on: July 15, 2015, 09:24:23 AM »
John, thank you very much for excellent guideline to the trace element EPMA analysis. I have downloaded attached materials, will look into details, and share it with customers and colleagues involved in the project. Much of it unfortunately would not be possible to perform at the moment, but it is great to know that there are possibilities to significantly improve using proper software.
Sergei

smatveev

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Re: Using CalcZAF To Teach EPMA
« Reply #14 on: July 17, 2015, 01:37:06 AM »
Of course it would only be a problem if you are analyzing all trace elements, since if a major element is present in the iteration that will dominate the matrix correction loop...
John, does it mean that iteration routine does not wait until every element is converged, but the first one to reach the difference limit? 
Sergei