Author Topic: Specifying Unanalyzed Elements For a Proper Matrix Correction  (Read 40992 times)

John Donovan

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #45 on: November 28, 2015, 07:43:34 AM »
Hi Andrew,
This is very useful stuff.  Thank-you.
john
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John Donovan

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #46 on: December 09, 2015, 12:52:21 PM »
I should mention that Julien Allaz's mineral re-normalization code has been translated from php to VB, so I will be able to implement this in Probe for EPMA at some point "real soon now"...
John J. Donovan, Pres. 
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AndrewLocock

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #47 on: January 19, 2016, 10:06:32 AM »
Here is an updated version of the Excel spreadsheet, which now properly deals with cases where both halogens and hydrogen are present in oxide materials.

John Donovan

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #48 on: July 06, 2018, 03:15:37 PM »
As many of you already know, there are two ways to specify unanalyzed elements *by difference* in the Probe for EPMA matrix corrections.  Here is a screen shot of the Calculation Options dialog in PFE showing the two "difference" methods:



So one could specify OH by difference by selecting the "element by difference" option, then selecting hydrogen as the element by difference, then making sure that the oxygen stoichiometry for hydrogen is changed from the default of 1 cation and 2 oxygens, to 1 hydrogen and 1 oxygen, in the Elements/Cations dialog.

Then the program will calculate OH by difference.   The other method is to use the "formula by difference" method where one specifies the unanalyzed elements as a formula, in this example, as OH, and the program adds them in automatically during the matrix calculation.  The benefit of including these unanalyzed elements by difference into the matrix correction, is that the presence (or absence) of the unanalyzed elements can affect the concentrations of the analyzed elements.  Thus affecting the calculation by difference. This is particularly import for so called "water by difference" measurements as discussed here:

http://probesoftware.com/smf/index.php?topic=922.0

As another example of elements by difference, one might be measuring traces in a matrix and have no need to measure the major elements. Say, traces in quartz or zircon, where one would measure the trace elements and merely specify the matrix elements as SiO2 or ZrSiO4 respectively, as a formula by difference. This is discussed here:

http://probesoftware.com/smf/index.php?topic=42.msg2568#msg2568

This formula by difference methods has worked well for when calculating without stoichiomeric oxygen, but after Gareth Seward and Marisa Acosta reported to us that this formula by difference method was not working correctly when oxygen was being calculated by stoichiomtry, we took a look and *finally* managed to find the problem and fixed the code.  This latest version of PFE will fix this issue.

Here is an example of an apatite sample where the students wanted to calculate OH by difference and calculate oxygen by stoichiometry:

Un   52 BMA-062-16fa_g25, Results in Elemental Weight Percents

SPEC:        O       H
TYPE:     FORM    FORM

AVER:   38.302    .038
SDEV:     .504    .041
 
ELEM:       Ca       P       S      Al      Fe      As      Ba       K
BGDS:      LIN     EXP     LIN     LIN     LIN     EXP     LIN     LIN
TIME:    25.00    8.00   25.00   25.00   30.00   60.00   90.00   90.00
BEAM:    30.06   30.06   30.06   30.06   30.06   99.04   99.04   99.04

ELEM:       Ca       P       S      Al      Fe      As      Ba       K   SUM 
   384  38.598  18.351    .032    .007    .181   -.076   -.008    .022 100.000
   385  38.462  18.005    .019   -.002    .167   -.003   -.001    .013 100.000
   386  38.210  18.037    .018    .002    .183    .030   -.007    .010 100.000
   387  38.235  17.974    .032    .008    .194   -.010   -.006    .003 100.000
   388  38.602  18.336    .037   -.007    .181    .030   -.004    .002 100.000
   389  37.771  18.007    .030    .011    .218    .074    .001    .059 100.000

AVER:   38.313  18.118    .028    .003    .187    .007   -.004    .018 100.000
SDEV:     .315    .175    .008    .007    .017    .051    .004    .021    .000
SERR:     .129    .072    .003    .003    .007    .021    .001    .009
%RSD:      .82     .97   28.02  213.60    9.28  676.66  -86.58  116.07
STDS:      285     285     327     336     160     662     835     336

STKF:    .3596   .1601   .2210   .1333   .0654   .5052   .7431   .0409
STCT:    738.0  4696.5  1704.0  6059.0  1413.2   583.1  3099.0   588.4

UNKF:    .3609   .1598   .0002   .0000   .0016   .0001   .0000   .0002
UNCT:    740.6  4689.7     1.9     1.1    34.1      .1     -.1     2.7
UNBG:      6.8    10.7     2.9    30.0    27.0    12.9     6.5    10.4

ZCOR:   1.0615  1.1335  1.1605  1.3622  1.1852  1.3270  1.4078   .9827
KRAW:   1.0036   .9986   .0011   .0002   .0242   .0001   .0000   .0045
PKBG:   110.25  468.43    1.67    1.04    2.27    1.01     .98    1.26
INT%:     ----    ----    ----    ----    ----    ----    ----    ----

TDI%:     .046    .488   4.073   1.487   2.693    ----    ----    ----
DEV%:       .4      .2    24.6     2.3     1.6    ----    ----    ----
TDIF:  LOG-LIN LOG-LIN LOG-LIN LOG-LIN LOG-LIN    ----    ----    ----
TDIT:    56.67   37.83   55.50   55.83   57.83    ----    ----    ----
TDII:     747.   4700.    4.56    31.2    61.7    ----    ----    ----
TDIL:     6.62    8.46    1.52    3.44    4.12    ----    ----    ----
 
ELEM:       Mn      Na      Sr       F      Sm      Nd      Cl       Y
BGDS:      LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN
TIME:    60.00   90.00   60.00   60.00   60.00   90.00   40.00   90.00
BEAM:    99.04   99.04   99.04   99.04   99.04   99.04   99.04   99.04

ELEM:       Mn      Na      Sr       F      Sm      Nd      Cl       Y   SUM 
   384    .302    .115    .050   2.828    .067    .102    .125    .337 100.000
   385    .294    .118    .049   3.490    .027    .115    .132    .297 100.000
   386    .332    .102    .043   3.229    .024    .085    .147    .257 100.000
   387    .361    .102    .057   3.950    .047    .055    .092    .229 100.000
   388    .309    .119    .041   3.970    .022    .091    .115    .295 100.000
   389    .313    .124    .042   4.081    .007    .126    .133    .370 100.000

AVER:     .318    .113    .047   3.591    .032    .096    .124    .298 100.000
SDEV:     .024    .009    .006    .497    .021    .025    .019    .051    .000
SERR:     .010    .004    .003    .203    .009    .010    .008    .021
%RSD:     7.63    8.01   13.19   13.84   65.51   26.11   15.42   17.23
STDS:       25     336     251     835    1011    1009     285    1016

STKF:    .7341   .0735   .4267   .1715   .5260   .5221   .0602   .4481
STCT:   4303.0  1786.2  3853.8   561.2  1133.9  3358.0   836.0  1076.4

UNKF:    .0026   .0005   .0004   .0071   .0002   .0007   .0011   .0026
UNCT:     15.4    12.7     3.6    23.1      .5     4.4    15.1     6.2
UNBG:      5.8    10.3     5.5     2.3     4.8    11.8     9.0     2.5

ZCOR:   1.2109  2.1625  1.1789  5.0816  1.4239  1.3990  1.1400  1.1620
KRAW:    .0036   .0071   .0009   .0412   .0004   .0013   .0181   .0057
PKBG:     3.67    2.24    1.66   11.03    1.10    1.37    2.68    3.45
INT%:     ----    ----    ----  -21.28   -6.97    -.95    -.31    ----

TDI%:     ----    ----    ----    ----    ----    ----    ----    ----
DEV%:     ----    ----    ----    ----    ----    ----    ----    ----
TDIF:     ----    ----    ----    ----    ----    ----    ----    ----
TDIT:     ----    ----    ----    ----    ----    ----    ----    ----
TDII:     ----    ----    ----    ----    ----    ----    ----    ----
TDIL:     ----    ----    ----    ----    ----    ----    ----    ----
 
ELEM:       Eu      Gd      Mg      La      Ce      Si
BGDS:      AVG     LIN     LIN     LIN     LIN     LIN
TIME:    60.00   60.00   90.00   60.00   60.00   60.00
BEAM:    99.04   99.04   99.04   99.04   99.04   99.04

ELEM:       Eu      Gd      Mg      La      Ce      Si   SUM 
   384    .029    .041    .045    .025    .133    .099 100.000
   385   -.005    .057    .044    .015    .112    .090 100.000
   386   -.008    .047    .039    .017    .097    .075 100.000
   387    .015    .029    .036    .005    .079    .058 100.000
   388    .024    .051    .041    .016    .129    .094 100.000
   389    .016    .056    .124    .023    .176    .295 100.000

AVER:     .012    .047    .055    .017    .121    .118 100.000
SDEV:     .015    .011    .034    .007    .033    .088    .000
SERR:     .006    .004    .014    .003    .014    .036
%RSD:   130.06   22.47   61.89   42.93   27.58   73.94
STDS:     1004    1005     160    1007    1001     160

STKF:    .5289   .5281   .0776   .5143   .5111   .1621
STCT:   1239.6  4995.6  3016.8 11742.1  3550.7  5699.0

UNKF:    .0001   .0003   .0003   .0001   .0009   .0010
UNCT:       .2     3.0    13.4     2.7     6.0    35.8
UNBG:      5.6    22.3    19.3    63.8    25.3     5.8

ZCOR:   1.4453  1.4722  1.5909  1.3981  1.3935  1.1629
KRAW:    .0002   .0006   .0044   .0002   .0017   .0063
PKBG:     1.04    1.14    1.69    1.04    1.24    7.09
INT%:    11.30  -17.82    ----   -5.08    -.03    ----

TDI%:     ----    ----    ----    ----    ----    ----
DEV%:     ----    ----    ----    ----    ----    ----
TDIF:     ----    ----    ----    ----    ----    ----
TDIT:     ----    ----    ----    ----    ----    ----
TDII:     ----    ----    ----    ----    ----    ----
TDIL:     ----    ----    ----    ----    ----    ----

Un   52 BMA-062-16fa_g25, Results in Oxide Weight Percents

SPEC:        O      HO
TYPE:     FORM    FORM

AVER:   -1.540    .638
SDEV:     .207    .685

ELEM:      CaO    P2O5     SO3   Al2O3     FeO   As2O3     BaO     K2O   SUM 
   384  54.007  42.049    .081    .014    .232   -.100   -.008    .026 100.000
   385  53.816  41.256    .048   -.004    .215   -.004   -.001    .016 100.000
   386  53.464  41.330    .044    .005    .235    .040   -.008    .013 100.000
   387  53.498  41.185    .081    .015    .249   -.014   -.007    .004 100.000
   388  54.011  42.014    .093   -.013    .233    .040   -.004    .003 100.000
   389  52.849  41.262    .075    .020    .280    .097    .001    .071 100.000

AVER:   53.608  41.516    .070    .006    .241    .010   -.005    .022 100.000
SDEV:     .441    .402    .020    .013    .022    .067    .004    .025    .000
SERR:     .180    .164    .008    .005    .009    .027    .002    .010
%RSD:      .82     .97   28.02  213.60    9.28  676.66  -86.58  116.07
STDS:      285     285     327     336     160     662     835     336

ELEM:      MnO    Na2O     SrO       F   Sm2O3   Nd2O3      Cl    Y2O3   SUM 
   384    .390    .155    .059   2.828    .077    .119    .125    .429 100.000
   385    .380    .158    .057   3.490    .031    .134    .132    .377 100.000
   386    .429    .138    .051   3.229    .028    .100    .147    .327 100.000
   387    .466    .138    .068   3.950    .054    .064    .092    .291 100.000
   388    .398    .161    .048   3.970    .025    .106    .115    .374 100.000
   389    .404    .167    .050   4.081    .008    .147    .133    .470 100.000

AVER:     .411    .153    .055   3.591    .037    .112    .124    .378 100.000
SDEV:     .031    .012    .007    .497    .025    .029    .019    .065    .000
SERR:     .013    .005    .003    .203    .010    .012    .008    .027
%RSD:     7.63    8.01   13.19   13.84   65.51   26.11   15.42   17.23
STDS:       25     336     251     835    1011    1009     285    1016

ELEM:    Eu2O3   Gd2O3     MgO   La2O3   Ce2O3    SiO2   SUM 
   384    .033    .047    .075    .029    .155    .213 100.000
   385   -.006    .066    .073    .017    .131    .192 100.000
   386   -.010    .054    .065    .020    .114    .160 100.000
   387    .018    .034    .059    .005    .093    .124 100.000
   388    .028    .059    .069    .019    .151    .202 100.000
   389    .019    .064    .205    .027    .206    .630 100.000

AVER:     .014    .054    .091    .020    .142    .254 100.000
SDEV:     .018    .012    .056    .008    .039    .187    .000
SERR:     .007    .005    .023    .003    .016    .077
%RSD:   130.06   22.47   61.89   42.93   27.58   73.94
STDS:     1004    1005     160    1007    1001     160

Notice that the oxygen concentration in the oxide output is negative.  This is because the program is also performing the correction for the halogen equivalent for oxygen in the matrix calculation!  Pretty cool!

If you'd like to learn more about the halogen equivalence for stoichiometric oxygen calculation feature see this post:

http://probesoftware.com/smf/index.php?topic=8.msg1127#msg1127
« Last Edit: April 12, 2020, 07:23:44 PM by John Donovan »
John J. Donovan, Pres. 
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AndrewLocock

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #49 on: September 28, 2018, 09:10:25 AM »
How does one delete previously-added unanalyzed elements from the list of elements?

Sometimes, one might want to try adding an unanalyzed element to set of analyses, as a test.
However, one may not want to keep such elements.
It would be nice to easily delete them, if one doesn't want them.
Thanks,
Andrew

John Donovan

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #50 on: September 28, 2018, 11:35:58 AM »
How does one delete previously-added unanalyzed elements from the list of elements?

Sometimes, one might want to try adding an unanalyzed element to set of analyses, as a test.
However, one may not want to keep such elements.
It would be nice to easily delete them, if one doesn't want them.

Hi Andrew,
It gets complicated because it's difficult to know what an element might be utilized for, so to be safe we only allow elements to be deleted from the Acquire! Elements/Cations dialog.   Sorry.
john
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Probeman

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #51 on: October 12, 2018, 03:37:43 PM »
This topic is entitled "Specifying Unanalyzed Elements For a Proper Matrix Correction", but it could just as well have been titled "Including unanalyzed elements for proper quantification of analyzed elements".

I recently responded to a question on the JEOL Listserver about how to add the carbonate molecule to a carbonate analysis using the JEOL software. I don't know the JEOL software, but then it was suggested performing the calculation off-line perhaps using Excel.  This is *not* a good idea as most of you know, because the matrix correction will be significantly wrong and the quantification of the analyzed elements will be significantly wrong.

If the total of the elements in the matrix correction is significantly under 100%, the matrix correction physics will be significantly wrong in most cases.  For example carbonates.

Here is an analysis of a standard dolomite where because the software knows that it is a standard, it can automatically specify the unanalyzed elements to get a correct quantification for the elements that were acquired:

St  141 Set   1 Dolomite (Harvard #105064), Results in Elemental Weight Percents
 
ELEM:       Ca      Mn       P      Mg      Fe       C       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    SPEC
BGDS:      LIN     LIN     LIN     LIN     LIN
TIME:    10.00   10.00   10.00   10.00   10.00     ---     ---
BEAM:    30.01   30.01   30.01   30.01   30.01     ---     ---

ELEM:       Ca      Mn       P      Mg      Fe       C       O   SUM 
    43  21.796    .081   -.040  13.417    .145  12.986  52.021 100.406
    44  21.698    .036    .025  13.332    .145  12.986  52.021 100.243
    45  21.876    .105    .024  13.396    .168  12.986  52.021 100.576
    46  22.000    .068   -.014  13.224    .145  12.986  52.021 100.430

AVER:   21.843    .073   -.001  13.342    .151  12.986  52.021 100.414
SDEV:     .128    .029    .032    .087    .011    .000    .000    .136
SERR:     .064    .014    .016    .043    .006    .000    .000
%RSD:      .58   39.60-2300.07     .65    7.43     .00     .00

PUBL:   21.841    .015    n.a.  13.195    .062  12.986  52.021 100.120
%VAR:      .01  383.93     ---    1.12  143.23     .00     .00
DIFF:     .001    .058     ---    .147    .089    .000    .000
STDS:      138     140     285     139     145     ---     ---

STKF:    .3789   .3969   .1600   .1957   .4258     ---     ---
STCT:   128.18  134.89   56.49   65.78  142.56     ---     ---

UNKF:    .2030   .0006   .0000   .0853   .0012     ---     ---
UNCT:    68.66     .20     .00   28.69     .42     ---     ---
UNBG:      .14     .77    1.00     .06     .49     ---     ---

ZCOR:   1.0763  1.2369  1.2287  1.5634  1.2161     ---     ---
KRAW:    .5356   .0015  -.0001   .4362   .0029     ---     ---
PKBG:   484.48    1.27    1.00  473.26    1.85     ---     ---

Note that carbon and oxygen were automatically loaded from the standard database into Probe for EPMA, because the software knows that it is a standard.  But what if this was an unknown carbonate?  Here is the same material (dolomite standard), but this time acquired as an unknown:

Un    6 Dolomite (Harvard #105064), Results in Elemental Weight Percents
 
ELEM:       Ca      Mn       P      Mg      Fe       C
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    SPEC
BGDS:      LIN     LIN     LIN     LIN     LIN
TIME:    10.00   10.00   10.00   10.00   10.00     ---
BEAM:    29.99   29.99   29.99   29.99   29.99     ---

ELEM:       Ca      Mn       P      Mg      Fe       C   SUM 
    47  21.220    .033   -.006  11.758    .135    .000  33.140
    48  21.136    .021    .010  11.939    .150    .000  33.258
    49  21.296    .055    .013  12.068    .164    .000  33.596
    50  21.292    .080    .067  12.059    .128    .000  33.626
    51  21.237    .066    .026  11.925    .117    .000  33.371
    52  21.278    .090    .017  11.796    .156    .000  33.337
    53  20.925    .121    .084  11.887    .161    .000  33.178

AVER:   21.198    .067    .030  11.919    .145    .000  33.358
SDEV:     .132    .034    .033    .119    .018    .000    .191
SERR:     .050    .013    .012    .045    .007    .000
%RSD:      .62   51.24  108.72    1.00   12.32     .00
STDS:      138     140     285     139     145     ---

STKF:    .3789   .3969   .1600   .1957   .4258     ---
STCT:   128.18  134.89   56.49   65.78  142.56     ---

UNKF:    .2047   .0006   .0002   .0852   .0012     ---
UNCT:    69.26     .19     .08   28.63     .41     ---
UNBG:      .13     .78     .97     .05     .51     ---

ZCOR:   1.0354  1.2003  1.2679  1.3995  1.1694     ---
KRAW:    .5403   .0014   .0015   .4353   .0029     ---
PKBG:   529.78    1.25    1.09  606.24    1.81     ---

First note the very low total (~33 wt.%). Because the software does not know that this is a carbonate, it cannot automatically specify the unanalyzed carbon and oxygen. And note that although Ca (Ka) isn't so affected (21.2 wt.% in the unknown vs. 21.8 wt.% in the standard), the Mg (Ka) is very much affected (11.9 wt.% in the unknown vs. 13.3 wt.% in the standard!).

Observe the differences in the magnitude of the matrix corrections for Ca (Ka) and Mg (Ka), in the line labeled ZCOR, and you will understand why.

So how to add in the missing carbonate molecule?  For the JEOL software Pete McSwiggen's suggestion is good because I assume that the JEOL software is including the specified unanalyzed elements in the matrix correction.

In Probe for EPMA one can do the same thing by first adding carbon as a unanalyzed element in the Elements/Cations dialog, then simply checking the Calculate with Stoichiometric Oxygen option, and finally specify 0.333 atoms of carbon per oxygen molecule as seen here:



Once that is done, the analysis proceeds as follows:

Un    6 Dolomite (Harvard #105064), Results in Elemental Weight Percents
 
ELEM:       Ca      Mn       P      Mg      Fe       C       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    STOI    CALC
BGDS:      LIN     LIN     LIN     LIN     LIN
TIME:    10.00   10.00   10.00   10.00   10.00     ---     ---
BEAM:    29.99   29.99   29.99   29.99   29.99     ---     ---

ELEM:       Ca      Mn       P      Mg      Fe       C       O   SUM 
    47  22.060    .034   -.006  13.130    .141  12.959  52.019 100.336
    48  21.965    .022    .010  13.349    .156  12.955  52.136 100.594
    49  22.130    .057    .012  13.486    .171  12.925  52.228 101.008
    50  22.123    .082    .065  13.482    .133  12.929  52.298 101.113
    51  22.071    .068    .025  13.327    .122  12.945  52.160 100.719
    52  22.122    .092    .016  13.162    .162  12.942  52.071 100.567
    53  21.748    .125    .081  13.286    .167  12.970  52.172 100.549

AVER:   22.031    .069    .029  13.318    .150  12.946  52.155 100.698
SDEV:     .137    .035    .032    .140    .019    .016    .093    .274
SERR:     .052    .013    .012    .053    .007    .006    .035
%RSD:      .62   51.26  108.66    1.05   12.33     .13     .18
STDS:      138     140     285     139     145     ---     ---

STKF:    .3789   .3969   .1600   .1957   .4258     ---     ---
STCT:   128.18  134.89   56.49   65.78  142.56     ---     ---

UNKF:    .2047   .0006   .0002   .0852   .0012     ---     ---
UNCT:    69.26     .19     .08   28.63     .41     ---     ---
UNBG:      .13     .78     .97     .05     .51     ---     ---

ZCOR:   1.0761  1.2369  1.2276  1.5637  1.2160     ---     ---
KRAW:    .5403   .0014   .0015   .4353   .0029     ---     ---
PKBG:   529.78    1.25    1.09  606.24    1.81     ---     ---

Note that now the concentrations and matrix corrections for Ca and Mg are correct.

By the way, the same calculation options will work for any carbonate such as calcite, magnesite, siderite, etc.
The only stupid question is the one not asked!

Probeman

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    • John Donovan
Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #52 on: October 13, 2018, 03:01:57 PM »
Since I mentioned the effect of not including water by difference as it affects the matrix correction in my JEOL Listserver post, I will "show my work" as to how the various unanalyzed elements affects the analyzed elements, as they are added to the matrix correction of a hydrous glass. For a publication reference see this paper:

https://link.springer.com/article/10.1007%2Fs00445-005-0003-z

In this example I selected an experimental glass from Withers, which nominally contains 4.9 wt.% H2O, but FTIR showed 5.06 wt%. Here is the analysis of this glass as an unknown with nothing but the analyzed elements:

Un   17 Withers-N5, Results in Elemental Weight Percents
 
ELEM:       Na       K      Cl      Ba       F      Ti      Fe      Mn      Ca      Si      Al      Mg       O       H       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    SPEC
BGDS:      MAN     LIN     LIN     LIN     LIN     LOW     MAN     LIN     MAN     MAN     MAN     MAN     EXP
TIME:    60.00   20.00   10.00   20.00   40.00   10.00   40.00   10.00   20.00   20.00   20.00   60.00     ---     ---     ---
BEAM:     9.98    9.98    9.98    9.98    9.98    9.98    9.98    9.98    9.98    9.98    9.98    9.98     ---     ---     ---

ELEM:       Na       K      Cl      Ba       F      Ti      Fe      Mn      Ca      Si      Al      Mg     O-D       H       O   SUM
   574   1.206   3.594    .218    .029    .046    .106   2.963    .058    .154  30.812   4.487   -.010     ---    .000    .000  43.664
   575   1.187   3.590    .221    .016    .045    .122   2.951    .076    .140  30.681   4.454   -.014     ---    .000    .000  43.469
   576   1.163   3.469    .192    .032    .054    .135   2.960    .080    .121  30.677   4.413   -.019     ---    .000    .000  43.275
   577   1.171   3.500    .276    .040    .059    .096   2.993    .056    .109  30.817   4.512   -.020     ---    .000    .000  43.610
   578   1.225   3.549    .276   -.013    .045    .071   3.001    .078    .108  30.727   4.451   -.012     ---    .000    .000  43.505
   579   1.218   3.559    .255   -.077    .038    .122   3.019    .079    .123  30.718   4.502   -.015     ---    .000    .000  43.541
   580   1.143   3.579    .238    .015    .048    .100   2.954    .052    .124  30.733   4.422   -.020     ---    .000    .000  43.387
   581   1.235   3.438    .264   -.019    .065    .116   2.933    .048    .144  30.823   4.443   -.015     ---    .000    .000  43.475
   582   1.170   3.501    .175   -.025    .043    .132   3.028    .049    .112  30.879   4.462   -.012     ---    .000    .000  43.514
   583   1.160   3.556    .233   -.061    .018    .145   2.995    .030    .136  30.874   4.465   -.017     ---    .000    .000  43.534
   584   1.183   3.491    .227    .004    .018    .122   2.956    .061    .125  30.945   4.416   -.017     ---    .000    .000  43.532
   585   1.148   3.503    .204    .029    .038    .119   2.978    .059    .153  30.943   4.465   -.015     ---    .000    .000  43.623

AVER:    1.184   3.527    .232   -.002    .043    .115   2.978    .060    .129  30.802   4.458   -.016     ---    .000    .000  43.511
SDEV:     .031    .051    .032    .038    .014    .020    .029    .015    .016    .095    .032    .003     ---    .000    .000    .105
SERR:     .009    .015    .009    .011    .004    .006    .009    .004    .005    .028    .009    .001     ---    .000    .000
%RSD:     2.59    1.43   13.87-1520.63   33.07   17.23     .99   25.47   12.47     .31     .72  -21.27     ---     .00     .00
STDS:      336     374     285     835     835      22     395      25     358     162     336      12     ---     ---     ---

STKF:    .0735   .1132   .0602   .7431   .1715   .5547   .6779   .7341   .1693   .2018   .1333   .4736     ---     ---     ---
STCT:   2447.9  2423.7   839.3  8520.6  2398.7  6097.6 14136.8 13590.2  2247.6 34290.6 23223.7 24410.3     ---     ---     ---

UNKF:    .0082   .0301   .0017   .0000   .0002   .0010   .0258   .0005   .0011   .2710   .0411  -.0001     ---     ---     ---
UNCT:    274.6   645.2    24.2     -.2     2.7    10.8   538.5     9.5    15.2 46037.3  7157.6    -6.4     ---     ---     ---
UNBG:     16.0    12.6     5.0    29.0     3.8     5.8    30.1    16.1     5.4   173.0   135.8    23.3     ---     ---     ---

ZCOR:   1.4355  1.1708  1.3315  1.3476  2.1906  1.1747  1.1530  1.1748  1.1290  1.1368  1.0853  1.2443     ---     ---     ---
KRAW:    .1122   .2662   .0289   .0000   .0011   .0018   .0381   .0007   .0068  1.3426   .3082  -.0003     ---     ---     ---
PKBG:    18.14   52.35    6.39    1.00    1.77    3.03   18.90    1.61    3.79  267.17   53.70     .72     ---     ---     ---
INT%:     ----    ----    ----   -3.80    ----    -.02    ----    ----    ----    ----    ----    ----     ---     ---     ---

If we calculate the above elemental analysis as oxide formulas (but still without oxygen included in the matrix correction), we get the following results:

Un   17 Withers-N5, Results in Oxide Weight Percents

ELEM:     Na2O     K2O      Cl     BaO       F    TiO2     FeO     MnO     CaO    SiO2   Al2O3     MgO     O-D     H2O       O   SUM
   574   1.625   4.330    .218    .033    .046    .177   3.812    .075    .216  65.918   8.479   -.016     ---    .000    .000  84.911
   575   1.600   4.324    .221    .018    .045    .203   3.797    .098    .196  65.639   8.415   -.024     ---    .000    .000  84.533
   576   1.568   4.179    .192    .035    .054    .225   3.808    .103    .169  65.629   8.338   -.032     ---    .000    .000  84.267
   577   1.578   4.216    .276    .045    .059    .161   3.851    .072    .153  65.928   8.526   -.033     ---    .000    .000  84.831
   578   1.651   4.276    .276   -.015    .045    .118   3.861    .100    .152  65.736   8.410   -.020     ---    .000    .000  84.588
   579   1.642   4.287    .255   -.086    .038    .204   3.884    .102    .171  65.716   8.507   -.025     ---    .000    .000  84.696
   580   1.540   4.311    .238    .017    .048    .166   3.800    .068    .173  65.749   8.356   -.034     ---    .000    .000  84.432
   581   1.665   4.141    .264   -.021    .065    .193   3.773    .062    .202  65.942   8.395   -.025     ---    .000    .000  84.656
   582   1.577   4.217    .175   -.028    .043    .220   3.895    .063    .157  66.061   8.431   -.020     ---    .000    .000  84.792
   583   1.564   4.283    .233   -.068    .018    .241   3.853    .039    .190  66.051   8.437   -.028     ---    .000    .000  84.813
   584   1.595   4.205    .227    .004    .018    .204   3.803    .079    .175  66.202   8.344   -.027     ---    .000    .000  84.829
   585   1.547   4.220    .204    .032    .038    .198   3.831    .076    .214  66.199   8.436   -.024     ---    .000    .000  84.971

AVER:    1.596   4.249    .232   -.003    .043    .192   3.831    .078    .181  65.897   8.423   -.026     ---    .000    .000  84.693
SDEV:     .041    .061    .032    .042    .014    .033    .038    .020    .023    .204    .060    .005     ---    .000    .000    .207
SERR:     .012    .018    .009    .012    .004    .010    .011    .006    .007    .059    .017    .002     ---    .000    .000
%RSD:     2.59    1.43   13.87-1520.63   33.07   17.23     .99   25.47   12.47     .31     .72  -21.27     ---     .00     .00
STDS:      336     374     285     835     835      22     395      25     358     162     336      12     ---     ---     ---

Note that total is much better, but the SiO2 concentration is only 65.9 wt.%.  Now we will recalculate the glass but this time include stoichiometric oxygen in the matrix correction:

Un   17 Withers-N5, Results in Oxide Weight Percents

ELEM:     Na2O     K2O      Cl     BaO       F    TiO2     FeO     MnO     CaO    SiO2   Al2O3     MgO     O-D     H2O       O   SUM
   574   2.177   4.249    .205    .033    .085    .179   3.990    .077    .225  70.085   9.983    .016     ---    .000    .000  91.303
   575   2.144   4.244    .207    .018    .083    .206   3.974    .101    .205  69.801   9.909    .008     ---    .000    .000  90.901
   576   2.102   4.100    .180    .036    .099    .227   3.986    .107    .179  69.809   9.823   -.002     ---    .000    .000  90.646
   577   2.115   4.136    .258    .045    .109    .162   4.031    .074    .163  70.096  10.042   -.004     ---    .000    .000  91.230
   578   2.211   4.195    .258   -.015    .082    .119   4.041    .103    .161  69.906   9.904    .012     ---    .000    .000  90.978
   579   2.200   4.206    .239   -.087    .069    .206   4.064    .105    .181  69.881  10.022    .007     ---    .000    .000  91.093
   580   2.067   4.230    .223    .017    .087    .168   3.978    .070    .182  69.960   9.850   -.004     ---    .000    .000  90.828
   581   2.234   4.061    .248   -.021    .120    .195   3.949    .064    .211  70.160   9.897    .007     ---    .000    .000  91.123
   582   2.116   4.137    .164   -.028    .079    .222   4.076    .065    .166  70.273   9.939    .012     ---    .000    .000  91.222
   583   2.100   4.202    .218   -.068    .033    .244   4.032    .040    .198  70.295   9.953    .003     ---    .000    .000  91.248
   584   2.141   4.125    .213    .004    .033    .206   3.981    .082    .184  70.459   9.840    .003     ---    .000    .000  91.271
   585   2.076   4.141    .191    .032    .070    .200   4.010    .079    .223  70.423   9.943    .007     ---    .000    .000  91.394

AVER:    2.140   4.169    .217   -.003    .079    .194   4.009    .080    .190  70.096   9.925    .005     ---    .000    .000  91.103
SDEV:     .055    .060    .030    .042    .026    .034    .039    .021    .022    .230    .069    .006     ---    .000    .000    .223
SERR:     .016    .017    .009    .012    .008    .010    .011    .006    .006    .066    .020    .002     ---    .000    .000
%RSD:     2.55    1.44   13.88-1522.79   33.11   17.23     .98   25.47   11.70     .33     .70  120.12     ---     .00     .00
STDS:      336     374     285     835     835      22     395      25     358     162     336      12     ---     ---     ---

Please note that by including the stoichiometric oxygen in the matrix correction the SiO2 concentration went from 65.9 wt.% to 70.09 wt.%.  This is because oxygen absorbs Si Ka more than Si.  So without stoichiometric oxygen in the matrix correction, the matrix is anomalously high in Si, which again, does not absorb Si Ka as much as oxygen, so the matrix correction for Si is underestimated.

But we still have a total of only 91.1 wt.%, so one might be forgiven to estimate the water by difference as 8.9 wt.%.  But one would be wrong because we haven't provided a correction for the ion migration of Na and the effect on the other elements. The TDI correction for Na in this glass is around 100% as seen here in this plot of log intensity vs. time:



So turning on the TDI correction we obtain these analyses:

Un   17 Withers-N5, Results in Oxide Weight Percents

ELEM:     Na2O     K2O      Cl     BaO       F    TiO2     FeO     MnO     CaO    SiO2   Al2O3     MgO     O-D     H2O       O   SUM
   574   4.117   4.182    .204    .033    .084    .179   3.989    .077    .224  69.392  10.084    .018     ---    .000    .000  92.582
   575   4.842   4.291    .207    .018    .082    .206   3.973    .101    .205  70.089  10.042    .010     ---    .000    .000  94.065
   576   4.255   3.997    .180    .036    .097    .227   3.985    .107    .179  69.839   9.930   -.001     ---    .000    .000  92.831
   577   4.575   4.261    .258    .045    .108    .162   4.029    .074    .163  69.847  10.167   -.002     ---    .000    .000  93.688
   578   4.550   4.211    .258   -.015    .081    .119   4.039    .103    .161  69.530  10.023    .013     ---    .000    .000  93.073
   579   4.687   4.256    .239   -.087    .068    .206   4.062    .105    .181  69.813  10.148    .008     ---    .000    .000  93.685
   580   4.257   4.207    .223    .017    .086    .168   3.976    .070    .182  69.621   9.960   -.003     ---    .000    .000  92.765
   581   4.968   4.191    .247   -.021    .118    .195   3.947    .064    .210  70.217  10.033    .008     ---    .000    .000  94.177
   582   4.447   4.237    .164   -.028    .079    .222   4.074    .065    .166  70.473  10.054    .013     ---    .000    .000  93.966
   583   4.547   4.070    .218   -.068    .032    .244   4.030    .040    .198  69.777  10.078    .004     ---    .000    .000  93.170
   584   4.524   4.049    .212    .004    .032    .206   3.979    .082    .184  70.249   9.959    .005     ---    .000    .000  93.486
   585   3.984   4.322    .191    .032    .069    .200   4.008    .078    .223  70.019  10.041    .008     ---    .000    .000  93.176

AVER:    4.479   4.190    .217   -.003    .078    .194   4.008    .080    .190  69.905  10.043    .007     ---    .000    .000  93.389
SDEV:     .288    .101    .030    .042    .026    .033    .039    .020    .022    .317    .072    .006     ---    .000    .000    .534
SERR:     .083    .029    .009    .012    .007    .010    .011    .006    .006    .091    .021    .002     ---    .000    .000
%RSD:     6.43    2.40   13.86-1523.55   33.08   17.23     .98   25.47   11.70     .45     .71   95.57     ---     .00     .00
STDS:      336     374     285     835     835      22     395      25     358     162     336      12     ---     ---     ---

Note that the Na concentration went from around 2.2 wt% to 4.4 wt.%, but the Si dropped slightly because the TDI effect on Si is usually an increase in intensity as the Na intensity drops due to ion migration under the electron beam.

Now based on our totals of around 93.4 wt.%, our water by difference estimate would be around 6.6 wt.%, but that isn't very close to the FTIR H2O measurement of 5.06 wt.%. So what's going on?  Well we have not yet included the water by difference into the matrix correction. Once we do that we obtain these results:

Un   17 Withers-N5, Results in Oxide Weight Percents

ELEM:     Na2O     K2O      Cl     BaO       F    TiO2     FeO     MnO     CaO    SiO2   Al2O3     MgO     O-D     H2O       O   SUM
   574   4.191   4.211    .205    .033    .086    .180   4.037    .078    .227  70.047  10.230    .020     ---   6.454    .000 100.000
   575   4.912   4.315    .207    .018    .084    .207   4.012    .102    .207  70.615  10.157    .011     ---   5.152    .000 100.000
   576   4.329   4.024    .181    .036    .100    .229   4.032    .108    .181  70.477  10.069    .001     ---   6.233    .000 100.000
   577   4.646   4.286    .259    .046    .110    .164   4.071    .075    .165  70.405  10.292   -.001     ---   5.483    .000 100.000
   578   4.627   4.239    .259   -.015    .083    .120   4.085    .104    .163  70.140  10.158    .015     ---   6.022    .000 100.000
   579   4.760   4.281    .240   -.088    .070    .207   4.104    .106    .182  70.371  10.272    .010     ---   5.485    .000 100.000
   580   4.333   4.236    .224    .018    .088    .169   4.024    .070    .184  70.264  10.101   -.001     ---   6.290    .000 100.000
   581   5.040   4.214    .248   -.021    .120    .196   3.985    .064    .212  70.735  10.146    .010     ---   5.052    .000 100.000
   582   4.513   4.261    .164   -.028    .080    .224   4.114    .065    .168  71.014  10.173    .015     ---   5.237    .000 100.000
   583   4.624   4.096    .218   -.069    .033    .246   4.075    .040    .200  70.382  10.213    .006     ---   5.936    .000 100.000
   584   4.597   4.074    .213    .004    .033    .207   4.022    .083    .186  70.832  10.085    .007     ---   5.658    .000 100.000
   585   4.050   4.350    .191    .033    .071    .202   4.053    .079    .225  70.631  10.176    .010     ---   5.929    .000 100.000

AVER:    4.552   4.216    .217   -.003    .080    .196   4.051    .081    .192  70.493  10.173    .009     ---   5.744    .000 100.000
SDEV:     .288    .100    .030    .043    .026    .034    .039    .021    .022    .284    .070    .007     ---    .469    .000    .000
SERR:     .083    .029    .009    .012    .008    .010    .011    .006    .006    .082    .020    .002     ---    .135    .000
%RSD:     6.33    2.38   13.86-1528.18   33.05   17.22     .97   25.48   11.66     .40     .69   76.35     ---    8.16     .00
STDS:      336     374     285     835     835      22     395      25     358     162     336      12     ---     ---     ---

Note that our SiO2 concentration went up slightly because we added additional oxygen (from H2O) into the matrix calculation, and so now our water by difference is around 5.7 wt.% which is quite close to our FTIR value of 5.06 wt.%.  If we had included other trace elements in the analysis, we would get even closer.

So, the lesson is, always include all the unanalyzed elements into the matrix correction, or you will have significant errors in the analyzed elements.  Excel is great, but it doesn't know physics!  Please let me know if anyone has any questions.
« Last Edit: October 13, 2018, 11:02:43 PM by Probeman »
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pvburger

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #53 on: March 08, 2019, 11:03:41 AM »
Does it make a difference if one includes oxygen as a specified element in the Elements/Cations menu of the Acquire! window prior to acquisition vs. simply selecting "Calculate with stoichiometric oxygen" under Calculation Options during the analysis step (following acquisition)?

I realize the output to the log may vary, but do the final concentrations saved from the Output menu differ? If so, is there any way to add "specified" oxygen as an element to a sample set that was initially acquired without it?

Cheers!

John Donovan

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #54 on: March 08, 2019, 11:33:18 AM »
Does it make a difference if one includes oxygen as a specified element in the Elements/Cations menu of the Acquire! window prior to acquisition vs. simply selecting "Calculate with stoichiometric oxygen" under Calculation Options during the analysis step (following acquisition)?

I realize the output to the log may vary, but do the final concentrations saved from the Output menu differ? If so, is there any way to add "specified" oxygen as an element to a sample set that was initially acquired without it?

Cheers!

Hi Paul,
This is a really good question because it relates to an important point about how stoichiometric oxygen is handled along with "excess oxygen" in Probe for EPMA (and CalcZAF for that matter).

Basically, stoichiometric oxygen or oxygen by stoichiometry are unrelated to acquisition because in either case they are "unanalyzed" or "specified" elements. So you can specify them prior to acquisition or after acquisition of the "analyzed" elements.

If you check the "Use Stoichiometric Oxygen" option in the Calculation Options dialog, the software will automatically add oxygen to your matrix and include it in the matrix corrections.

But sometimes, we will want to specify some additional or "excess" oxygen as part of our analysis. For example your Fe is specified as FeO, but you are measuring a magnetite specimen. There is some discussion here on this:

https://probesoftware.com/smf/index.php?topic=223.msg1002#msg1002

But the bottom line is that yes, you can have oxygen calculated by stoichiometry, *and* you can add oxygen as a "specified" element for dealing with excess or oxygen deficits. Oxygen as an unanalyzed element is added, just as you would with any other unanalyzed elements, from the Elements/Cations dialog, but leaving the x-ray line blank.

Now all of this changes when you have oxygen as an analyzed element!  When oxygen is being analyzed for (and when the oxidation state of Fe is uncertain this is actually a very good idea), the software will automatically subtract the stoichiometric oxygen from the measured oxygen to obtain the so called "excess" oxygen. This post describes that situation:

https://probesoftware.com/smf/index.php?topic=197.msg888#msg888

This can get complicated but play around with your samples, and if you can, try analyzing some standards as unknowns, e.g., magnetite, and it should become clear. But feel free to post some examples of what you are trying to accomplish if you have any questions at all.
John J. Donovan, Pres. 
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Probeman

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #55 on: July 02, 2019, 11:09:46 AM »
Most of us understand the effects of "unanalyzed" elements in the matrix correction and how it is important to include these elements either by specification, difference or by stoichiometry to other analyzed elements, in order to obtain an accurate matrix correction.

For example the issue of unanalyzed water in hydrous glasses, where one gets a results with a total of say 95% and one might be forgiven to think that, OK, I've got 5 wt% H2O there because 100 - 95 = 5 in Excel.  But that would be wrong because Excel doesn't know anything about matrix correction physics.  In fact what we see when we specify water by difference is described in this and other posts in this topic:

https://probesoftware.com/smf/index.php?topic=92.msg7701#msg7701

Basically adding oxygen (and hydrogen) to our glass matrix correction results in a significant change in the concentration of other elements.  In a generic example of a silicate glass, the Si (and other element) concentrations increases significantly.  Why is this? Because it turns out that Si Ka is not well absorbed by Si atoms, but they are well absorbed by oxygen atoms!  Once the matrix correction "knows" about the extra oxygen (water), the absorption correction increases correspondingly.

So in our generic example of a 95% total in a hydrous glass, once we add H2O by difference and include it in the matrix correction, because the Si (and other elements) increase by about 1%, we instead obtain about 4% H2O by difference.  This effect was described in the Roman et al. paper referenced here:

https://probesoftware.com/smf/index.php?topic=61.msg4303#msg4303

Now this makes some intuitive sense to me because Si Ka is a fairly low energy emission line and therefore fairly well absorbed by other elements, but I never expected this to be the case for Fe Ka at 6.4 keV!

Here's an example for a magnetite sample where the Fe is expressed, as we usually do in EPMA, as FeO:

Un   96 7138_PPO-2_Mgt4_HO-1, 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     EXP     LIN     MAN     MAN
TIME:    40.00  120.00   40.00   80.00   30.00   30.00   80.00  120.00     ---
BEAM:    45.93   45.93   45.93   45.93   45.93   45.93   45.93   45.93     ---

ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O   SUM 
   146  60.944   1.463    .058   5.329    .265    .422    .375   1.542  23.842  94.240

AVER:   60.944   1.463    .058   5.329    .265    .422    .375   1.542  23.842  94.240
SDEV:     .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
SERR:     .000    .000    .000    .000    .000    .000    .000    .000    .000
%RSD:      .00     .00     .00     .00     .00     .00     .00     .00     .00
STDS:      396     396      14      22      23      25     396     396     ---

STKF:    .1836   .0330   .4101   .5547   .6328   .7341   .3060   .0469     ---
STCT:   1119.3  3499.0  4307.2  9290.4  8344.6 14435.6  1338.8  1992.0     ---

UNKF:    .5710   .0066   .0004   .0548   .0028   .0040   .0043   .0088     ---
UNCT:   3481.1   701.1     4.3   917.6    37.1    77.9    18.9   373.9     ---
UNBG:     12.2    47.8     2.8    32.9    15.3    29.2     6.1    29.4     ---

ZCOR:   1.0674  2.2108  1.4127   .9728   .9416  1.0658   .8682  1.7520     ---
KRAW:   3.1102   .2004   .0010   .0988   .0044   .0054   .0141   .1877     ---
PKBG:   286.31   15.65    2.55   28.88    3.43    3.67    4.10   13.70     ---
INT%:      .00    ----    ----    ----  -15.76    ----   -1.38    ----     ---

As one can see our Fe concentration is 60.944 and our total is 94.240. So we're missing about 5% of something and that something of course is mostly the excess oxygen in the Fe2O3 molecule in magnetite. Now how much of an effect can this ~5% missing oxygen have on our Fe concentration? What would you guess?  I wouldn't have guessed this much:

Un   96 7138_PPO-2_Mgt4_HO-1, Results in Elemental Weight Percents
 
ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    DIFF
BGDS:      MAN     MAN     MAN     MAN     EXP     LIN     MAN     MAN
TIME:    40.00  120.00   40.00   80.00   30.00   30.00   80.00  120.00     ---
BEAM:    45.93   45.93   45.93   45.93   45.93   45.93   45.93   45.93     ---

ELEM:       Fe      Mg      Si      Ti       V      Mn      Cr      Al       O   SUM 
   146  61.421   1.451    .057   5.379    .267    .425    .383   1.532  29.085 100.000

AVER:   61.421   1.451    .057   5.379    .267    .425    .383   1.532  29.085 100.000
SDEV:     .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
SERR:     .000    .000    .000    .000    .000    .000    .000    .000    .000
%RSD:      .00     .00     .00     .00     .00     .00     .00     .00     .00
STDS:      396     396      14      22      23      25     396     396     ---

STKF:    .1836   .0330   .4101   .5547   .6328   .7341   .3060   .0469     ---
STCT:   1119.3  3499.0  4307.2  9290.4  8344.6 14435.6  1338.8  1992.0     ---

UNKF:    .5710   .0066   .0004   .0548   .0028   .0040   .0044   .0088     ---
UNCT:   3481.6   701.6     4.3   918.5    37.1    77.9    19.1   374.1     ---
UNBG:     11.8    47.3     2.8    32.0    15.3    29.2     5.9    29.2     ---

ZCOR:   1.0756  2.1904  1.4061   .9808   .9506  1.0740   .8773  1.7396     ---
KRAW:   3.1106   .2005   .0010   .0989   .0044   .0054   .0143   .1878     ---
PKBG:   296.98   15.83    2.54   29.68    3.43    3.67    4.25   13.80     ---
INT%:      .00    ----    ----    ----  -15.75    ----   -1.36    ----     ---

Holy cow!  Our Fe concentration went from 60.944 to 61.421 which is almost 0.5 wt% absolute. And note how the ZCOR (matrix correction) for Fe Ka went from 1.0674 to 1.0756.  But even more mind blowing is to compare the *other* elements we measured: Mg, Ti, Al, etc.  What happened to them?  Well they went slightly *down* in concentration!  Why? Because they are more absorbed by Fe than by O.  It just goes to show you that one cannot intuit physics, you have to just run the darn calculation.

Of course we really should calculate the excess oxygen in our magnetites/ilmenites using a ferric/ferrous calculation (and more on that later), but the oxygen by difference calculation demonstrates that once we obtain our ferric/ferrous ratio, we really need to calculate the excess oxygen from that and specify it in Probe for EPMA, to obtain a more accurate Fe concentration for our mineral thermodynamic calculations.

Now, I'm no geologist but perhaps one should then recalculate our ferric/ferrous ratios, this time using our improved Fe concentration. Again, more on this later...
« Last Edit: July 02, 2019, 12:07:28 PM by Probeman »
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Probeman

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #56 on: July 11, 2019, 12:39:23 PM »
I'm no geologist but I think this is a cool trick to deal with missing OH in (some/all?) amphiboles.

So here is a tremolite (asbestos) analysis I did recently for the CDC:

Un   13 AZ asbestos gr6, Results in Oxide Weight Percents

ELEM:     Na2O    SiO2     K2O   Al2O3     FeO     MgO     CaO      Cl    TiO2       F     MnO     ZnO       O      HO   SUM 
   642   -.016  57.171    .112    .186   3.613  22.006  12.782    .004   -.044   -.063    .185    .028    .000    .000  95.963
   643    .006  57.423    .086    .203   3.307  22.143  12.787    .000   -.031    .049    .215    .009    .000    .000  96.199
   644    .008  57.522    .078    .182   3.437  22.184  12.780    .004   -.015   -.027    .178    .026    .000    .000  96.358
   645    .060  57.454    .073    .163   3.168  22.240  12.908    .003    .012   -.071    .175    .029    .000    .000  96.213
   646    .088  57.484    .079    .053   3.012  22.158  13.087   -.003   -.036   -.047    .138   -.041    .000    .000  95.972

AVER:     .029  57.411    .086    .157   3.307  22.146  12.869    .002   -.023   -.032    .178    .010    .000    .000  96.141
SDEV:     .043    .139    .016    .060    .233    .086    .134    .003    .022    .049    .028    .030    .000    .000    .170
SERR:     .019    .062    .007    .027    .104    .039    .060    .001    .010    .022    .012    .013    .000    .000
%RSD:   146.89     .24   18.18   38.14    7.04     .39    1.04  159.31  -97.92 -151.68   15.48  295.57  223.61     .00
STDS:      336     162     374     336     162     162     162     285      22     835      25     660     ---     ---

Note that the total is quite low due to the missing OH molecule.  Now looking up the formula for tremolite we see this:  Ca2Mg5Si8O22(OH)2. So there are 2 OH molecules for every 8 Si atoms or 0.25 hydroxyls for every Si atom.

Next we add hydrogen as an unanalyzed elements in the Elements/Cations dialog like this, being sure to specify 1 hydrogen and 1 oxygen, to obtain the hydroxyl molecule:



Next we go into the Calculation Options dialog and specify oxygen by stoichiometry, and .25 hydrogens (as hydroxyl), to 1 Si atom as seen here:



Now when we calculate the composition we get:

Un   13 AZ asbestos gr6, Results in Oxide Weight Percents

ELEM:     Na2O    SiO2     K2O   Al2O3     FeO     MgO     CaO      Cl    TiO2       F     MnO     ZnO       O      HO   SUM 
   642   -.014  57.329    .112    .187   3.634  22.208  12.820    .004   -.044   -.065    .186    .028    .000   4.057 100.442
   643    .009  57.587    .086    .204   3.326  22.349  12.826    .000   -.032    .050    .216    .009    .000   4.075 100.705
   644    .011  57.682    .078    .183   3.456  22.389  12.819    .004   -.015   -.028    .179    .026    .000   4.082 100.866
   645    .063  57.613    .073    .164   3.186  22.446  12.946    .003    .012   -.073    .176    .029    .000   4.077 100.717
   646    .091  57.650    .079    .054   3.030  22.366  13.126   -.003   -.036   -.048    .139   -.042    .000   4.080 100.486

AVER:     .032  57.572    .086    .158   3.326  22.352  12.908    .002   -.023   -.033    .179    .010    .000   4.074 100.643
SDEV:     .043    .141    .016    .060    .234    .088    .134    .003    .022    .049    .028    .030    .000    .010    .176
SERR:     .019    .063    .007    .027    .105    .039    .060    .001    .010    .022    .012    .013    .000    .004
%RSD:   136.72     .24   18.19   38.03    7.03     .39    1.04  159.31  -97.92 -151.40   15.48  295.57 -651.92     .24
STDS:      336     162     374     336     162     162     162     285      22     835      25     660     ---     ---

Not only is our total now very close to 100%, but note how the Si and Mg compositions have changed, because now the matrix effect of that 4 wt% OH was included in the matrix calculations.
« Last Edit: July 11, 2019, 12:41:22 PM by Probeman »
The only stupid question is the one not asked!

Brian Joy

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #57 on: July 11, 2019, 01:21:49 PM »
I'm no geologist but I think this is a cool trick to deal with missing OH in (some/all?) amphiboles.

So here is a tremolite (asbestos) analysis I did recently for the CDC:

Un   13 AZ asbestos gr6, Results in Oxide Weight Percents

ELEM:     Na2O    SiO2     K2O   Al2O3     FeO     MgO     CaO      Cl    TiO2       F     MnO     ZnO       O      HO   SUM 
   642   -.016  57.171    .112    .186   3.613  22.006  12.782    .004   -.044   -.063    .185    .028    .000    .000  95.963
   643    .006  57.423    .086    .203   3.307  22.143  12.787    .000   -.031    .049    .215    .009    .000    .000  96.199
   644    .008  57.522    .078    .182   3.437  22.184  12.780    .004   -.015   -.027    .178    .026    .000    .000  96.358
   645    .060  57.454    .073    .163   3.168  22.240  12.908    .003    .012   -.071    .175    .029    .000    .000  96.213
   646    .088  57.484    .079    .053   3.012  22.158  13.087   -.003   -.036   -.047    .138   -.041    .000    .000  95.972

AVER:     .029  57.411    .086    .157   3.307  22.146  12.869    .002   -.023   -.032    .178    .010    .000    .000  96.141
SDEV:     .043    .139    .016    .060    .233    .086    .134    .003    .022    .049    .028    .030    .000    .000    .170
SERR:     .019    .062    .007    .027    .104    .039    .060    .001    .010    .022    .012    .013    .000    .000
%RSD:   146.89     .24   18.18   38.14    7.04     .39    1.04  159.31  -97.92 -151.68   15.48  295.57  223.61     .00
STDS:      336     162     374     336     162     162     162     285      22     835      25     660     ---     ---

Note that the total is quite low due to the missing OH molecule.  Now looking up the formula for tremolite we see this:  Ca2Mg5Si8O22(OH)2. So there are 2 OH molecules for every 8 Si atoms or 0.25 hydroxyls for every Si atom.

Next we add hydrogen as an unanalyzed elements in the Elements/Cations dialog like this, being sure to specify 1 hydrogen and 1 oxygen, to obtain the hydroxyl molecule:



Next we go into the Calculation Options dialog and specify oxygen by stoichiometry, and .25 hydrogens (as hydroxyl), to 1 Si atom as seen here:



Now when we calculate the composition we get:

Un   13 AZ asbestos gr6, Results in Oxide Weight Percents

ELEM:     Na2O    SiO2     K2O   Al2O3     FeO     MgO     CaO      Cl    TiO2       F     MnO     ZnO       O      HO   SUM 
   642   -.014  57.329    .112    .187   3.634  22.208  12.820    .004   -.044   -.065    .186    .028    .000   4.057 100.442
   643    .009  57.587    .086    .204   3.326  22.349  12.826    .000   -.032    .050    .216    .009    .000   4.075 100.705
   644    .011  57.682    .078    .183   3.456  22.389  12.819    .004   -.015   -.028    .179    .026    .000   4.082 100.866
   645    .063  57.613    .073    .164   3.186  22.446  12.946    .003    .012   -.073    .176    .029    .000   4.077 100.717
   646    .091  57.650    .079    .054   3.030  22.366  13.126   -.003   -.036   -.048    .139   -.042    .000   4.080 100.486

AVER:     .032  57.572    .086    .158   3.326  22.352  12.908    .002   -.023   -.033    .179    .010    .000   4.074 100.643
SDEV:     .043    .141    .016    .060    .234    .088    .134    .003    .022    .049    .028    .030    .000    .010    .176
SERR:     .019    .063    .007    .027    .105    .039    .060    .001    .010    .022    .012    .013    .000    .004
%RSD:   136.72     .24   18.19   38.03    7.03     .39    1.04  159.31  -97.92 -151.40   15.48  295.57 -651.92     .24
STDS:      336     162     374     336     162     162     162     285      22     835      25     660     ---     ---

Not only is our total now very close to 100%, but note how the Si and Mg compositions have changed, because now the matrix effect of that 4 wt% OH was included in the matrix calculations.

Hi John,

This is not correct.  Amphiboles generally have around 2 wt% H2O assuming that no F-, Cl-, or O2- substitutes for OH-.  For charge balance, you should have specified 2 hydrogens per oxygen.  Also, note that Al3+ can substitute for Si4+ on the tetrahedral sites, and so it is not sound practice to specify a given number of OH- per Si4+.

Brian
Brian Joy
Queen's University
Kingston, Ontario
JEOL JXA-8230

AndrewLocock

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #58 on: July 11, 2019, 01:25:56 PM »
Hello,
The general idea of calculating the hydroxyl content in advance of the matrix corrections is a good one, but I should draw your attention to some problems with the discussion immediately above.

1) The concentrations of the elements should be expressed as neutral oxides.
Thus, the method should report percent-by-weight of H2O, not the hydroxyl moiety.
For both of the average tremolite compositions discussed, the amount of H2O(!) should be 2.19 wt%.
This corresponds to two hydroxyl units per formula unit in each of these cases:
(K0.016) (Ca1.923Mn0.021Fe0.019Na0.008)Σ1.971 (Mg4.605Fe0.367Al0.026Zn0.002)Σ5 (Si8.006)Σ8.006 O22 (OH)2
(K0.016) (Ca1.921Fe0.037Mn0.021Na0.008)Σ1.987 (Mg4.627Fe0.349Al0.021Zn0.002)Σ4.999 (Si7.995Al0.005)Σ8 O22 (OH)2
The final totals are thus 98.4 to 98.8 wt%.

2) Many (most) amphibole species do not have exactly 8 Si per formula unit.
One could instead use the ratio of H to oxygen for those amphiboles that are assumed to have only hydroxyl present (no oxo-substitution, and no significant F or Cl present).
The ratio would be 2 H for 24 oxygen, or 0.0833333 H for 1 O.

3) A minor point, but in my view, negative values of the measured elements should be automatically set to zero, prior to averaging.

Best regards,
Andrew



Probeman

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Re: Specifying Unanalyzed Elements For a Proper Matrix Correction
« Reply #59 on: July 11, 2019, 01:55:31 PM »
As I said, I'm no geologist, so please explain why the formula for tremolite is given as Ca2Mg5Si8O22(OH)2

http://www.webmineral.com/data/Tremolite.shtml#.XSeiNP57laQ

I only assumed Si might be a valid element to ratio hydrogen to because there's almost no Al in this composition.  Maybe this only works for tremolite?

My main point was just to show the matrix effect of including OH or H2O, on the other measured elements. What is your suggestion for adding in the missing hydroxyl or water to improve the matrix correction accuracy?  Just specify 2% H2O?
« Last Edit: July 11, 2019, 02:17:30 PM by Probeman »
The only stupid question is the one not asked!