### Author Topic: Specifying Unanalyzed Elements For a Proper Matrix Correction  (Read 25232 times)

#### John Donovan

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##### Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #105 on: August 19, 2019, 04:13:36 pm »
OK, now on to Probe for EPMA.   We think the implementation of the ferrous/ferric calculation (from Droop, 1987) is pretty good, but please download the latest version (12.7.1) and let us know what you think.  The CalcZAF implementation is described here:

https://probesoftware.com/smf/index.php?topic=691.msg8592#msg8592

So let's take an example of hematite. Calculating all iron as FeO we get these results:

Un    3 Hematite, Results in Elemental Weight Percents

ELEM:       Fe       O
TYPE:     ANAL    CALC
BGDS:      LIN
TIME:    10.00     ---
BEAM:    30.00     ---

ELEM:       Fe       O   SUM
29  68.992  19.766  88.758
30  69.126  19.805  88.931
31  68.758  19.699  88.457

AVER:   68.959  19.757  88.715
SDEV:     .186    .053    .240
SERR:     .108    .031
%RSD:      .27     .27
STDS:       39     ---

STKF:    .6810     ---
STCT:   228.06     ---

UNKF:    .6566     ---
UNCT:   219.89     ---
UNBG:      .48     ---

ZCOR:   1.0503     ---
KRAW:    .9642     ---
PKBG:   456.58     ---

Un    3 Hematite, Results in Oxide Weight Percents

ELEM:      FeO       O   SUM
29  88.758    .000  88.758
30  88.931    .000  88.931
31  88.457    .000  88.457

AVER:   88.715    .000  88.715
SDEV:     .240    .000    .240
SERR:     .138    .000
%RSD:      .27  -91.65
STDS:       39     ---

Note the low totals (~88%) due to the missing ferric oxygen.  Now we specify the ferrous/ferric calculation and the mineral cations and oxygen (2 and 3 respectively for hematites) as seen here:

and re-calculating we now obtain these results:

Un    3 Hematite, Results in Elemental Weight Percents

ELEM:       Fe       O
TYPE:     ANAL    CALC
BGDS:      LIN
TIME:    10.00     ---
BEAM:    30.00     ---

ELEM:       Fe       O   SUM
29  70.168  30.155 100.323
30  70.305  30.213 100.518
31  69.930  30.052  99.982

AVER:   70.134  30.140 100.274
SDEV:     .190    .081    .271
SERR:     .109    .047
%RSD:      .27     .27
STDS:       39     ---

STKF:    .6810     ---
STCT:   228.06     ---

UNKF:    .6566     ---
UNCT:   219.89     ---
UNBG:      .48     ---

ZCOR:   1.0682     ---
KRAW:    .9642     ---
PKBG:   456.58     ---

Ferrous/Ferric Calculation Results:
Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3
29       1.000        .000     100.323      10.052
30       1.000        .000     100.518      10.071
31       1.000        .000      99.982      10.017

AVER:        1.000        .000     100.274      10.047

Un    3 Hematite, Results in Oxide Weight Percents

ELEM:      FeO       O   SUM
29  90.271  10.052 100.323
30  90.447  10.071 100.518
31  89.965  10.017  99.982

AVER:   90.228  10.047 100.274
SDEV:     .244    .027    .271
SERR:     .141    .016
%RSD:      .27     .27
STDS:       39     ---

Our totals are now much better but because we included this excess oxygen in the matrix correction as suggested by Brian Joy, even more impressive is that our Fe went from 68.959 to 70.134 wt%!

We also added this ferrous/ferric output to the User Specified Output options as seen here:

so now these results can be output to Excel as usual:

« Last Edit: August 19, 2019, 05:56:38 pm by John Donovan »
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#### Probeman

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##### Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #106 on: September 11, 2019, 02:38:22 pm »
Here's a "real world" example of a titanium magnetite with the ferrous/ferric excess oxygen calculation in Probe for EPMA using the method of Droop (1987) to calculate the excess oxygen from ferric iron. This excess oxygen is then added into the matrix correction for improved accuracy. The output below also includes oxides and sum of cations also as specified in the Calculation Options dialog.

Un   30 8400 Mgt Trav In-Out
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 50.0  Beam Size =    0
(Magnification (analytical) =  20000),        Beam Mode = Analog  Spot
(Magnification (default) =     1000, Magnification (imaging) =    100)
Image Shift (X,Y):                                       -2.00,   3.00

Formula Based on Sum of Cations = 3.00   Oxygen Calc. by Stoichiometry
Number of Data Lines:   6             Number of 'Good' Data Lines:   6
First/Last Date-Time: 07/23/2019 02:12:20 PM to 07/23/2019 02:29:56 PM

Average Total Oxygen:       28.684     Average Total Weight%:  100.294
Average Calculated Oxygen:  28.684     Average Atomic Number:   20.135
Average Excess Oxygen:        .000     Average Atomic Weight:   31.696
Average ZAF Iteration:        3.00     Average Quant Iterate:     4.00

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Excess Oxygen From Ferric Iron Calculated and Included in the Matrix Correction
Charge Balance Method of Droop (1987), Total Cations= 3.00, Total Oxygens= 4.00

Un   30 8400 Mgt Trav In-Out, Results in Elemental Weight Percents

ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    CALC
BGDS:      MAN     MAN     MAN     MAN     LIN     LIN     MAN     MAN
TIME:    40.00  140.00   40.00   80.00   30.00   30.00   88.00  141.00     ---
BEAM:    50.32   50.32   50.32   50.32   50.32   50.32   50.32   50.32     ---

ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O   SUM
72  60.751   1.862    .019   6.903    .309    .403    .054   1.270  28.664 100.234
73  60.644   1.863    .075   6.872    .333    .407    .059   1.258  28.657 100.170
74  60.946   1.871    .021   6.884    .295    .405    .056   1.255  28.732 100.464
75  60.505   1.856    .028   6.918    .323    .420    .056   1.260  28.584  99.950
76  60.954   1.876    .016   6.951    .335    .422    .043   1.251  28.776 100.623
77  60.805   1.858    .023   6.949    .301    .404    .044   1.249  28.693 100.325

AVER:   60.768   1.864    .030   6.913    .316    .410    .052   1.257  28.684 100.294
SDEV:     .175    .008    .022    .032    .017    .008    .007    .008    .066    .235
SERR:     .071    .003    .009    .013    .007    .003    .003    .003    .027
%RSD:      .29     .41   73.90     .47    5.40    2.06   12.65     .61     .23
STDS:      395      12      14      22      23      25      24     396     ---

STKF:    .6779   .4736   .4101   .5547   .6328   .7341   .6400   .0469     ---
STCT:   6812.2 53482.2  7089.5 14540.1 13304.5 22081.3  4697.4  3264.8     ---

UNKF:    .5649   .0085   .0002   .0703   .0033   .0038   .0006   .0072     ---
UNCT:   5676.3   964.8     3.7  1841.7    69.6   114.7     4.3   503.0     ---
UNBG:     20.5    79.1     5.5    52.0    25.2    49.5     9.6    48.0     ---

ZCOR:   1.0758  2.1821  1.4034   .9839   .9547  1.0761   .8885  1.7401     ---
KRAW:    .8333   .0180   .0005   .1267   .0052   .0052   .0009   .1541     ---
PKBG:   277.35   13.19    1.68   36.42    3.77    3.32    1.45   11.48     ---
INT%:      .00    ----    ----    ----  -17.39    -.03  -10.90     .00     ---

Ferrous/Ferric Calculation Results:
Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3
72        .458      42.390      39.749       3.983
73        .455      42.482      39.494       3.957
74        .460      42.324      40.100       4.018
75        .456      42.333      39.459       3.954
76        .458      42.468      39.953       4.003
77        .458      42.388      39.828       3.990

AVER:         .458      42.397      39.764       3.984

Un   30 8400 Mgt Trav In-Out, Results in Oxide Weight Percents

ELEM:      FeO     MgO    SiO2    TiO2    V2O3     MnO   Cr2O3   Al2O3       O   SUM
72  78.156   3.087    .041  11.515    .454    .520    .079   2.400   3.983 100.234
73  78.019   3.090    .161  11.464    .491    .526    .086   2.377   3.957 100.170
74  78.407   3.103    .044  11.484    .433    .523    .081   2.371   4.018 100.464
75  77.839   3.078    .059  11.539    .476    .542    .082   2.382   3.954  99.950
76  78.418   3.110    .034  11.594    .492    .545    .063   2.363   4.003 100.623
77  78.225   3.080    .050  11.591    .442    .522    .065   2.359   3.990 100.325

AVER:   78.177   3.091    .065  11.531    .465    .530    .076   2.375   3.984 100.294
SDEV:     .225    .013    .048    .054    .025    .011    .010    .015    .025    .235
SERR:     .092    .005    .020    .022    .010    .004    .004    .006    .010
%RSD:      .29     .41   73.90     .47    5.40    2.06   12.65     .61     .64
STDS:      395      12      14      22      23      25      24     396     ---

Un   30 8400 Mgt Trav In-Out, Results Based on Sum of 3 Cations

ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O   SUM
72   2.381    .168    .001    .315    .013    .016    .002    .103   3.921   6.921
73   2.377    .168    .006    .314    .014    .016    .002    .102   3.921   6.921
74   2.384    .168    .002    .314    .013    .016    .002    .102   3.922   6.922
75   2.378    .168    .002    .317    .014    .017    .002    .103   3.921   6.921
76   2.380    .168    .001    .316    .014    .017    .002    .101   3.922   6.922
77   2.382    .167    .002    .317    .013    .016    .002    .101   3.923   6.923

AVER:    2.380    .168    .002    .316    .014    .016    .002    .102   3.922   6.922
SDEV:     .002    .000    .002    .001    .001    .000    .000    .001    .001    .001
SERR:     .001    .000    .001    .001    .000    .000    .000    .000    .000
%RSD:      .10     .24   73.96     .46    5.41    2.06   12.76     .74     .02

Note that if we did *not* include the calculation of excess oxygen in the matrix correction our oxides and formula would look like this:

Un   30 8400 Mgt Trav In-Out, Results in Oxide Weight Percents

ELEM:      FeO     MgO    SiO2    TiO2    V2O3     MnO   Cr2O3   Al2O3       O   SUM
72  77.687   3.107    .037  11.434    .451    .517    .074   2.412    .000  95.718
73  77.554   3.109    .158  11.383    .487    .523    .080   2.388    .000  95.684
74  77.933   3.123    .041  11.402    .430    .520    .076   2.383    .000  95.908
75  77.374   3.098    .056  11.458    .472    .539    .076   2.393    .000  95.467
76  77.946   3.130    .031  11.512    .489    .542    .058   2.375    .000  96.083
77  77.755   3.100    .047  11.509    .439    .519    .059   2.371    .000  95.799

AVER:   77.708   3.111    .062  11.450    .461    .527    .071   2.387    .000  95.776
SDEV:     .221    .013    .048    .054    .025    .011    .010    .015    .000    .210
SERR:     .090    .005    .020    .022    .010    .004    .004    .006    .000
%RSD:      .28     .41   78.00     .47    5.41    2.06   13.52     .61 -167.33
STDS:      395      12      14      22      23      25      24     396     ---

Un   30 8400 Mgt Trav In-Out, Results Based on Sum of 3 Cations

ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O   SUM
72   2.379    .170    .001    .315    .013    .016    .002    .104   3.376   6.376
73   2.375    .170    .006    .313    .014    .016    .002    .103   3.379   6.379
74   2.382    .170    .002    .313    .013    .016    .002    .103   3.374   6.374
75   2.376    .170    .002    .316    .014    .017    .002    .104   3.378   6.378
76   2.378    .170    .001    .316    .014    .017    .002    .102   3.376   6.376
77   2.380    .169    .002    .317    .013    .016    .002    .102   3.377   6.377

AVER:    2.378    .170    .002    .315    .014    .016    .002    .103   3.377   6.377
SDEV:     .002    .000    .002    .001    .001    .000    .000    .001    .002    .002
SERR:     .001    .000    .001    .001    .000    .000    .000    .000    .001
%RSD:      .10     .24   78.05     .46    5.41    2.06   13.63     .74     .06

Of course the oxygen formula is low, but note the effect of this "missing oxygen" on the concentrations of the other elements. E.g., without the excess oxygen in the matrix correction, the Fe and Ti concentrations went down, but the Mg and Al concentrations went up!
« Last Edit: September 11, 2019, 03:26:57 pm by Probeman »
The only stupid question is the one not asked!

#### Probeman

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##### Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #107 on: February 10, 2020, 10:14:23 pm »
Mike Dungan, Andrew Locock and I fixed a problem with some oxide compositions in the ferric/ferric excess oxygen calculation as seen here:

Ferrous/Ferric Calculation Results:
Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3
37        .387      44.824      31.498       3.156
38        .387      44.633      31.339       3.140

AVER:         .387      44.729      31.419       3.148

Un    6 CH-19_Ox99_Mgt Core-1, Results in Oxide Weight Percents

ELEM:      FeO     MgO    TiO2    V2O3     MnO   Cr2O3   Al2O3    SiO2     CaO       O   SUM
37  73.166   2.152  18.583    .543    .586    .006   1.835    .053    .014   3.156 100.093
38  72.832   2.159  18.500    .553    .574    .002   1.906    .043    .014   3.140  99.723

AVER:   72.999   2.156  18.541    .548    .580    .004   1.870    .048    .014   3.148  99.908
SDEV:     .236    .005    .059    .008    .008    .003    .051    .007    .000    .011    .261
SERR:     .167    .003    .042    .005    .006    .002    .036    .005    .000    .008
%RSD:      .32     .23     .32    1.39    1.45   69.25    2.70   14.77    1.72     .36
STDS:      395      12      22      23      25      24     306      14     306     ---

Un    6 CH-19_Ox99_Mgt Core-1, Results Based on Sum of 3 Cations

ELEM:       Fe      Mg      Ti       V      Mn      Cr      Al      Si      Ca       O   SUM
37   2.251    .118    .514    .016    .018    .000    .080    .002    .001   4.000   7.000
38   2.248    .119    .514    .016    .018    .000    .083    .002    .001   4.000   7.000

AVER:    2.250    .118    .514    .016    .018    .000    .081    .002    .001   4.000   7.000
SDEV:     .002    .001    .000    .000    .000    .000    .002    .000    .000    .000    .000
SERR:     .002    .000    .000    .000    .000    .000    .002    .000    .000    .000
%RSD:      .10     .46     .09    1.62    1.22   69.07    2.93   14.55    1.49     .00

This change now properly handles oxides such as Al2O3, V2O3, Cr2O3, etc. You can update PFE anytime.
« Last Edit: February 11, 2020, 07:32:25 am by Probeman »
The only stupid question is the one not asked!

#### John Donovan

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##### Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #108 on: June 29, 2020, 09:34:18 am »
We've recently been working with Julien Allaz to fix the way in which the oxygen-halogen correction is applied to standards in Probe for EPMA as first reported by Ben Wade:

https://probesoftware.com/smf/index.php?topic=1247.msg9305#msg9305

During that time we realized that these recent halogen correction issues for standards (when oxygen is calculated by stoichiometry rather than a fixed concentration), are somewhat similar to the excess oxygen calculation using the Droop method of charge balance (hey- it's all about charge balance!). Again only for standard samples, when oxygen is calculated by stoichiometry (as opposed to added by fixed concentration from the standard database).

Previously, for the excess oxygen from ferric iron calculation, we simply did not allow one to perform this excess oxygen calculation for standards (only for unknown samples). But we realized yesterday that it's the same issue in that a double correction is applied for standards if the excess (or deficit) oxygen is already included in the standard database, and the excess (or deficit) oxygen correction for ferric oxygen (or halogen equivalence) is applied in Probe for EPMA, *and* the oxygen in the standard is calculated by stocihiometry.  Whew!

So what we did was enable the calculation of excess oxygen for standards (just as we have had for the halogen correction), so if the standard analysis is using the default fixed oxygen concentration from the standard database, all is well.  This can be seen is this output:

Excess Oxygen From Ferric Iron was not Included in the Matrix Correction (because oxygen was not calculated by cation stoichiometry)

St  395 Set   1 Magnetite U.C. #3380, Results in Elemental Weight Percents

ELEM:        F      Fe      Al      Mg      Mn       O
TYPE:     ANAL    ANAL    SPEC    SPEC    SPEC    SPEC
BGDS:      LIN     LIN
TIME:    20.00   20.00     ---     ---     ---     ---
BEAM:    29.98   29.98     ---     ---     ---     ---

ELEM:        F      Fe      Al      Mg      Mn       O   SUM
10    .051  71.844    .201    .072    .054  27.803 100.025
11    .073  72.195    .201    .072    .054  27.803 100.398
12    .026  72.209    .201    .072    .054  27.803 100.365

AVER:     .050  72.083    .201    .072    .054  27.803 100.263
SDEV:     .023    .207    .000    .000    .000    .000    .207
SERR:     .014    .119    .000    .000    .000    .000
%RSD:    46.70     .29     .00     .00     .00     .00

PUBL:     n.a.  72.080    .201    .072    .054  27.803 100.210
%VAR:      ---   (.00)     .00     .00     .00     .00
DIFF:      ---   (.00)    .000    .000    .000    .000
STDS:      835     395     ---     ---     ---     ---

STKF:    .1715   .6779     ---     ---     ---     ---
STCT:    57.18  228.22     ---     ---     ---     ---

UNKF:    .0002   .6779     ---     ---     ---     ---
UNCT:      .07  228.22     ---     ---     ---     ---
UNBG:      .32     .49     ---     ---     ---     ---

ZCOR:   2.2854  1.0633     ---     ---     ---     ---
KRAW:    .0013  1.0000     ---     ---     ---     ---
PKBG:     1.23  466.16     ---     ---     ---     ---

Ferrous/Ferric Calculation Results:
Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3
10        .000        .000        .000        .000
11        .000        .000        .000        .000
12        .000        .000        .000        .000

AVER:         .000        .000        .000        .000

But in the case where the user changes the standard analysis calculation to calculate oxygen by stoichiometry, the program will now zero out the excess oxygen (just as it now does for the deficit oxygen from halogens), and not perform a double correction as seen here:

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Oxygen Equivalent from Halogens (F/Cl/Br/I) was Subtracted in the Matrix Correction
Excess Oxygen From Ferric Iron Calculated and Included in the Matrix Correction
Charge Balance Method of Droop (1987), Total Cations= 3.00, Total Oxygens= 4.00

St  395 Set   1 Magnetite U.C. #3380, Results in Elemental Weight Percents

ELEM:        F      Fe      Al      Mg      Mn       O
TYPE:     ANAL    ANAL    SPEC    SPEC    SPEC    CALC
BGDS:      LIN     LIN
TIME:    20.00   20.00     ---     ---     ---     ---
BEAM:    29.98   29.98     ---     ---     ---     ---

ELEM:        F      Fe      Al      Mg      Mn       O   SUM
10    .051  71.838    .201    .072    .054  27.742  99.957
11    .073  72.206    .201    .072    .054  27.908 100.514
12    .026  72.215    .201    .072    .054  27.859 100.427

AVER:     .050  72.086    .201    .072    .054  27.836 100.299
SDEV:     .023    .215    .000    .000    .000    .085    .300
SERR:     .014    .124    .000    .000    .000    .049
%RSD:    46.75     .30     .00     .00     .00     .31

PUBL:     n.a.  72.080    .201    .072    .054  27.803 100.210
%VAR:      ---   (.01)     .00     .00     .00     .12
DIFF:      ---   (.01)    .000    .000    .000    .033
STDS:      835     395     ---     ---     ---     ---

STKF:    .1715   .6779     ---     ---     ---     ---
STCT:    57.18  228.22     ---     ---     ---     ---

UNKF:    .0002   .6779     ---     ---     ---     ---
UNCT:      .07  228.22     ---     ---     ---     ---
UNBG:      .32     .49     ---     ---     ---     ---

ZCOR:   2.2865  1.0633     ---     ---     ---     ---
KRAW:    .0013  1.0000     ---     ---     ---     ---
PKBG:     1.23  466.16     ---     ---     ---     ---

Ferrous/Ferric Calculation Results:
Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3
10        .674      30.092      69.266       6.940
11        .678      29.937      69.966       7.010
12        .671      30.591      69.252       6.938

AVER:         .674      30.207      69.495       6.963

So now, the code for dealing with this is seen here:

Code: [Select]
`If sample(1).Type% = 1 Thenanalysis.WtPercents!(chan%) = ConvertTotalToExcessOxygen!(Int(1), sample(), stdsample())If UseOxygenFromHalogensCorrectionFlag And sample(1).OxideOrElemental% = 1 ThenIf analysis.WtPercents!(chan%) < 0# Then analysis.WtPercents!(chan%) = 0#  ' zero out oxygen deficit from standard databaseEnd IfIf sample(1).FerrousFerricCalculationFlag And sample(1).OxideOrElemental% = 1 ThenIf analysis.WtPercents!(chan%) > 0# Then analysis.WtPercents!(chan%) = 0#  ' zero out oxygen excess from standard databaseEnd If' For unknowns, use specified oxygen weight percentElseanalysis.WtPercents!(chan%) = stdsample(1).ElmPercents!(ip%)End If`
One possible remaining issue is when one has both halogens and ferric iron present in a standard, and one tries to calculate oxygen by stoichiometry, the excess/deficit oxygen might not be handled perfectly. In this case, we would just say, simply use the default to calculate oxygen elementally (fixed concentration from the standard database) and all will be well.  But I think it will work, because if both the oxygen-halogen correction *and* the ferric iron calculation correction are turned on, you'll get a zero value for excess/deficit oxygen, so it should all work.

Remember, in all cases, the calculations for unknown samples are handled just fine. This is all pretty complicated we know, but please ask us any questions you may have.

In the meantime, update Probe for EPMA from the Help menu and these options are all available now.
« Last Edit: June 29, 2020, 10:08:29 pm by John Donovan »
John J. Donovan, Pres.
(541) 343-3400

"Not Absolutely Certain, Yet Reliable"