Questions about MAN background use

[glennpoirier]

Hi John,
I'm using the newest version of PfE (11.6.9) and I'm getting some odd behaviour when I'm trying to assign man fits, I'm getting some errors about missing standards at the start, but then when I get to the window and verify the fits and hit OK the display cycles through  all the elements  generates a warning  ("Warning no man standards have been assigned yet to calculate the man background fit  on spectrometer 2 on crystal TAP at 20 keV"  which is odd because Na on spectro 2 is not part of this particular sample) and stops. The only way to get out of the MAN assignment and fit window is to hit cancel, which I assume cancels the man fit. Is this a bug or is my run not set up properly?

Cheers

Glenn

[John Donovan]

I'm using the newest version of PfE (11.6.9) and I'm getting some odd behaviour when I'm trying to assign man fits, I'm getting some errors about missing standards at the start, but then when I get to the window and verify the fits and hit OK the display cycles through  all the elements  generates a warning  ("Warning no man standards have been assigned yet to calculate the man background fit  on spectrometer 2 on crystal TAP at 20 keV"  which is odd because Na on spectro 2 is not part of this particular sample) and stops. The only way to get out of the MAN assignment and fit window is to hit cancel, which I assume cancels the man fit. Is this a bug or is my run not set up properly?

Hi Glenn,
This is because of Julien's issue above where he had multiple samples with different elements, but he still wants all of the MAN fits to be assigned to *all* MAN elements in *all* samples in the run.

So, yes. The new behavior of the software is to go through all samples in the entire run (if they are not disabled), and check for missing MAN assignments.  So if you are getting warnings for a sample you don't care about, just disable it and re-load the MAN fits. Or acquire at least one MAN standard for that element with missing MAN standards.

Sorry for the change in behavior, but because of the potential of multiple sample setups with different or duplicate MAN elements, I had to check all samples in the probe run (unless they have been disabled).
john

[Probeman]

Hi Glenn,
I was thinking that instead of disabling the offending samples so they don't get included in the MAN fit assignments, one could also just use the disable quant flag for the specific element causing the problem in the Elements/Cations dialog.  But when I look closer, although I am checking for the disable acquisition flag, I am not checking for the disable quant flag.

But I wonder if you can utilize the disable acquisition flag for the offending element, in the offending samples, to avoid the missing MAN standard warnings?   I note that one can disable acquisition on a specific element on a specific sample, so long as it doesn't have any data...
john

[Ery Hughes]

Hi there,

I'm using MAN backgrounds for analysis of hydrous basaltic glasses as it reduces the analysis time by half reducing the chance of beam damage (also running TDI in case there still is beam damage). Just wanted to check that a specified by difference element (H in this case) is included in the iterative calculation of the mean atomic number?

Thanks!

Ery

[John Donovan]

Hi there,

I'm using MAN backgrounds for analysis of hydrous basaltic glasses as it reduces the analysis time by half reducing the chance of beam damage (also running TDI in case there still is beam damage). Just wanted to check that a specified by difference element (H in this case) is included in the iterative calculation of the mean atomic number?

Thanks!

Ery

Hi Ery,
Good question.  Here is how it works:

The average Z for the standards used in the MAN fit is calculated (as expected) based on the composition of the standards as defined in the standard.mdb database.  So as long as the standard composition never changes, the average Z will always be the same.

However for unknowns, we have to utilize the average Z from the calculated composition. So, the average Z calculation for MAN includes the measured elements and also the specified elements whether they be by stoichiometry or by difference. So yes.

More details are in my recent trace MAN paper:

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

Of equal importance is the fact that when calculating water (or any element) by difference (or by stoichiometry), one must include these elements by difference in the matrix correction, as is the case with Probe for EPMA. See the paper attached to this post, comparing water by difference included and not included in the matrix correction:

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

john

[John Donovan]

Hi Ery,
I just realized that you can see the calculated Z-bar or average Z in two places in Probe for EPMA. First here in the log window output:

Un   27 MAM IW2 C4-ext-1
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 20.0  Beam Size =   10
(Magnification (analytical) =   8000),        Beam Mode = Analog  Spot
(Magnification (default) =     1267, Magnification (imaging) =   1267)
Image Shift (X,Y):                                         .00,    .00
Number of Data Lines:   6             Number of 'Good' Data Lines:   6
First/Last Date-Time: 03/13/2007 06:29:57 PM to 03/13/2007 06:49:54 PM
WARNING- Using Exponential Off-Peak correction for p ka
WARNING- Using Time Dependent Intensity (TDI) Element Correction

Average Total Oxygen:       43.852     Average Total Weight%:  100.331
Average Calculated Oxygen:  43.852     Average Atomic Number:   13.324
Average Excess Oxygen:        .000     Average Atomic Weight:   22.489
Average ZAF Iteration:        3.00     Average Quant Iterate:     3.00

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction

And also here in the Analyze! window:



The average Z value will change visibly as the specified concentrations or elements by difference are modified.

[Ben Buse]

Hi,

I've just noticed something. When you have elements on multiple spectrometers - and your viewing the MAN curves individually (not something you would normally do - only for testing, comparing spectrometers.. etc). The MAN is wrong for those standards which contain a high abundance of the element on multiple spectrometers.

e.g. If I view Al individually  for Al2O3 and have it on 3 spectrometers.
Total is 189.46 (3*47.5 plus oxygen 47.075) and z-bar is 11.761

Whereas if I aggregate the spectrometers - Total is 100% and Z-BAR is correct 10.666

This is not a problem for analysis - for you'd never use something with 190% total, BUT something to be aware of when doing such tests

Ben

[Ben Buse]

Hi John,

I think I missing something obvious - but using the custom output #8 (MAN) - what's the difference in units for intensity - I can't get them to match.





The intensity scale is difference. But if I divide rawcnt by seconds and nA it does not help (e.g. 8/10sec/20nA).

Also 520 Al-metal looks different

Thanks

Ben

[John Donovan]

Hi Ben,
The difference is that the raw MAN intensities output to a file are *not* corrected for continuum absorption, but the intensities in the MAN plot are corrected for continuum absorption.

Try comparing the raw intensities to the raw plot, by unchecking the Correct for Continuum Absorption checkbox.

That doesn't mean that I have gotten something mixed up somewhere!   
john

[John Donovan]

I've just noticed something. When you have elements on multiple spectrometers - and your viewing the MAN curves individually (not something you would normally do - only for testing, comparing spectrometers.. etc). The MAN is wrong for those standards which contain a high abundance of the element on multiple spectrometers.

e.g. If I view Al individually  for Al2O3 and have it on 3 spectrometers.
Total is 189.46 (3*47.5 plus oxygen 47.075) and z-bar is 11.761

Whereas if I aggregate the spectrometers - Total is 100% and Z-BAR is correct 10.666

This is not a problem for analysis - for you'd never use something with 190% total, BUT something to be aware of when doing such tests

Hi Ben,
Yes, when one has a 190% total, how should one calculate the matrix correction (or average Z) for such a non-physical situation?  Answer: any way you feel like! 

The reason the average Z calculation is off when the spectrometers are not aggregated in your example is (I think) because you have several times the Al (from three spectrometers) relative to the specified oxygen (from the standard database), so the average Z is biased towards Al (Z = 13), rather than oxygen (Z = 8 ). 

Try analyzing it in Analyze! using the stoichiometric oxygen option (in Calculation Options dialog).
john

[Ben Buse]

Hi John,

The difference is that the raw MAN intensities output to a file are *not* corrected for continuum absorption, but the intensities in the MAN plot are corrected for continuum absorption.

Thanks  - that makes sense - and was it!

Try analyzing it in Analyze! using the stoichiometric oxygen option (in Calculation Options dialog).
john

Thanks - that worked - keeping Al and O in proportion - great suggestion

Ben

[Ben Buse]

Hi,

I just found what I was looking for - on the MAN output to excel you have both

rawcnt: data uncorrected for absorption.
corcnt: data corrected for absorption

Thanks

Ben

[John Donovan]

I just found what I was looking for - on the MAN output to excel you have both

rawcnt: data uncorrected for absorption.
corcnt: data corrected for absorption

Yes, that's right.  In fact it also outputs all the matrix corrections for those MAN standards so you could also work backwards from the corrected counts...

Note that years ago I originally tried a continuum specific correction from NIST (because the continuum correction should be different from the bulk correction due to the anisotropy of the continuum emission), but it gave worse results than the bulk correction, so the bulk matrix correction term is what we currently use for the MAN continuum absorption correction.
john

[Heather Lowers]

Is there an option to output the intercept, slope, curvature, Rel % Deviation for the MAN fits for all the elements in a run, and maybe even which standards are being used?  Playing around with different standards, off peak positions, forcing straight line versus not, etc.  Be nice to have these values easily tabulated.

[Probeman]

Is there an option to output the intercept, slope, curvature, Rel % Deviation for the MAN fits for all the elements in a run, and maybe even which standards are being used?  Playing around with different standards, off peak positions, forcing straight line versus not, etc.  Be nice to have these values easily tabulated.

Currently these parameters are output from the Output | Save Custom Analysis Output | Save Custom Analysis Format #8 (MAN):

LINE        Data file line number
SNUM        Sample number (standard number)
SNAM        Sample name (standard name)
ZBAR        Sample average atomic number
RAWCNT      Raw count intensity
CORCNT      Corrected count intensity (absorption corrected)
ZEDCOR      Atomic number correction factor
ABSCOR      Absorption correction factor
FLUCOR      Fluorescence correction factor
ZAFCOR      Total ZAF correction factor
ONTIM       On-peak (MAN) counting time
BEAM        Beam current in nA
BEAMCUR     Beam current (combined condition samples)

And if you put the software in DebugMode from the Output menu, you will see this output in the log window:

Elements:
      si      fe      mg      ca       p      al      na      ba       k      ti

MAN Assignments:
     835     835     336     374     336      12     835     336     358     336
      12      12     374     835     374      14      12     358     835     358
      22      14     835      14     835      27      14      12      12     374
      27      22      14      22      12      28      22      14      14     835
      28      28      22      28      14     285      27      27      22      12
     285     285      27       0      22       0      28      28      27      14
       0       0      28       0      27       0     285     160      28      27
       0       0       0       0      28       0       0     285     160      28
       0       0       0       0       0       0       0       0     285     160
       0       0       0       0       0       0       0       0       0     285
BackgroundTypes:
     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
MAN Fit Orders:
       2       2       2       2       2       2       2       2       2       2
MAN Absorption Correction Flags:
      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1
MAN Counts:
    74.1    21.7    13.9    29.4     3.5    16.7    22.1    44.1    30.3     1.3
    26.1     6.2    16.2    92.0     3.6    27.2     9.4    47.4    81.6     1.6
    51.7     6.1    22.4    26.3     9.3    32.1     6.8    42.3    25.5     1.9
    55.3     9.5    13.9    43.0     3.3    30.3     8.1    44.1    24.0     8.8
    58.4    15.3    15.7    59.7     3.0    29.4     8.3    93.4    39.2     1.2
    50.0     8.4    17.6      .0     5.5      .0     7.8    94.5    53.7     1.2
      .0      .0    14.5      .0     6.9      .0     9.2    49.2    54.8     3.4
      .0      .0      .0      .0     6.3      .0      .0    55.5    32.0     3.5
      .0      .0      .0      .0      .0      .0      .0      .0    34.4     1.4
      .0      .0      .0      .0      .0      .0      .0      .0      .0     2.0

MAN Fit Coefficients:
 -14.766 -3.2199 -6.5750 -8.5227 -.40542 30.2930 .112198 -.54570 -5.1947 .052925
 5.84314 .946438 2.68385 3.62923 .482494 -.80475 1.00449 3.86722 3.24887 .100007
 -.05119 -.00766 -.02100 -.02692 -.00311 .097303 .019536 -.00100 -.02401 .002169