# Changeset 2980

Ignore:
Timestamp:
Aug 9, 2017 12:11:13 PM (5 years ago)
Message:

fix

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1 edited

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Removed
• ## Tutorials/FitPeaks/Fit Peaks.htm

 r2653 Von Dreele Von Dreele 7 1035 vondreele 10 1125 2014-07-21T14:48:00Z 2016-07-28T18:11:00Z 27 3023 17232 2017-08-09T17:10:00Z 24 3016 17194 Argonne National Laboratory 143 40 20215 20170 16.00 Print 156 Clean Clean {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:1; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:0 0 0 0 0 0;} mso-font-signature:-536870145 1107305727 0 0 415 0;} @font-face {font-family:Calibri; mso-generic-font-family:swiss; mso-font-pitch:variable; mso-font-signature:-536870145 1073786111 1 0 415 0;} mso-font-signature:-536859905 -1073732485 9 0 511 0;} @font-face {font-family:Tahoma; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

and the plot window will show the powder pattern

and the plot window will show the powder pattern

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Step 2: Select Limits

more data than we need, so it is helpful to cut down the range. Click on the Limits item in the GSAS-II data tree. The small window is repainted. Use the new column of entry boxes to set Tmin and Tmax to 4 and Limits item in the GSAS-II data tree. Use the New: row of entry boxes to set 27.5. Notice on the plot that the limit lines have moved to these positions; the green lower limit is just below the 1st peak and the red upper limit is in a wide gap between peaks. You may also drag the limit lines to the desired location. Limits may also be set by a left mouse click on a data point for the lower limit or a right click on a data point for the upper limit.

minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin
and Tmax to 4 and 27.5. Notice on the plot that the limit lines have moved to these positions; the green lower limit is just below the 1st peak and the red upper limit is in a wide gap between peaks. You may also drag the limit lines to the desired location or place them by a left mouse click on a data point for the lower limit or a right click on a data point for the upper limit.

Step 3: Determine Peak Positions

style='font:7.0pt "Times New Roman"'>      Click on the Peak List item in the GSAS-II data tree. This creates an empty window of peak positions (the Peak List item in the Limits window is erased). At this point it is wise to zoom in on the data that will be used for indexing.

minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree. This creates an empty window of peak positions (the Limits window is erased). At this point it is wise to zoom in on the data that will be used for indexing.

Peak Fitting in the Peak List window select Auto search. The plot window will immediately show that all peaks were picked with a blue vertical line on each one

in the menu select Auto search. The plot window will immediately show that all peaks were picked with a blue vertical line on each one

and peaks are shown in the Peak List window in order of increasing 2Q.

auto'>and peaks are shown in the Peak List window in order of increasing 2Q.

There flags turned on by default. Use the menu item Peak Fitting/PeakFit on the Peak List window. Do NOT use the Calculate/Refine menu item in the GSAS-II data tree window; that it to be used for Rietveld/Pawley refinements. You will be asked to save the current project before the fit will proceed; change directory if desired and provide a suitable name (we assume LaB6). A window will show the progress of the refinement and will close when the least-squares fit is complete (usually very fast). The plot is updated with the fit, the peak list window is updated with the new peak values and a summary of the refinement is shown on the console window as well.

minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak Fitting/Peakfit. Do NOT use the Calculate/Refine menu item; that it to be used for Rietveld/Pawley refinements. You will be asked to save the current project before the fit will proceed; change directory if desired and provide a suitable name (we assume LaB6). A window will show the progress of the refinement and will close when the least-squares fit is complete (usually very fast). The plot is updated with the fit, the peak list window is updated with the new peak values and a summary of the refinement is shown on the console window as well.

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y key to turn on all refinement flags (n would turn them off).

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y key to turn on all refinement flags (n would turn them off).

Next, repeat the refinement using the Peak Fitting/PeakFit menu item in the Peak List window.

Now, select peak widths for click the refinement flags for sigma and/or gamma in the Peak List window.   Method 2: preferably, the LS refinement of peak widths can be constrained to follow an instrumental broadening equation as described below. Note - one cannot refine ALL peak widths using both individual sigma & gamma values AND instrumental broadening terms at the same time.

widths can be constrained to follow an instrumental broadening equation as described below. Note - one cannot refine ALL peak widths using both individual sigma & gamma values AND instrumental broadening terms at the same time.

Instrumental Parameters item in the data tree. This opens a window for peak profile terms and also creates a new plot window showing the instrument profile resolution curve.

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Instrumental Parameters item in the data tree. This opens a window for peak profile terms and also creates a new plot window showing the instrument profile resolution curve.

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The plot window shows the resolution curves values for the peaks in Peak List. Select the refine flag checkbox for Gaussian U, V, W, and Lorentzian X, Y.

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>U, V, W, and Lorentzian X, Y.

Peak List item in the data tree and then refine using the Peak Fitting/PeakFit menu item. At this point a good fit should be seen by zooming in on individual peaks. For example see

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List item in the data tree and then refine using the Peak Fitting/Peakfit menu item. At this point a good fit should be seen by zooming in on individual peaks. For example see

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Notice that the peak position is slightly to the right of the peak top. This is a consequence of the peak asymmetry arising from axial divergence in the diffractometer. The Rwp is ~6% as shown on the console window. Again the Peak List entries are all updated with new values and those in Peak List entries are all updated with new values and those in Instrument Parameters are also updated.

class=SpellE>autoindexing. It is found in the Index Peak List item in the data tree. In the initially empty window created by this action, use menu item Operations/Load/Reload to copy the fitted peaks from the Peak List.

minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peak List item in the data tree. In the initially empty window created by this action, use menu item Operations/Load/Reload to copy the fitted peaks from the Peak List.

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Note that by default all peaks are selected to be used. You

Select the Unit Cells List data item. This brings up a window for indexing and cell refinement options

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells List data item. This brings up a window for indexing and cell refinement options

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For the most rapid search (since we know the right answer), select Cubic-P and launch the search using menu item Cell Index/Refine/Index Cell. The search then runs and the console shows a running list of possible cells as they are found; the sorted by M20 list of possible matching cells is shown in the Unit Cells List window

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Cubic-P and launch the search using menu item Cell Index/Refine/Index Cell. The search then runs and the console shows a running list of possible cells as they are found; the sorted by M20 list of possible matching cells is shown in the Unit Cells List window

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Step 7. Review Cell Choices

Review the list of cells associated with the Unit Cells List data item. Note that as one selects a unit cell, the generated reflections for that cell are shown in the plot with dashed red lines. Sliding the cursor over these lines shows a small popup window with the indexed hkl for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å generates very many lines with no corresponding peaks (NB: this solution might not always show up!)

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Unit Cells List data item. Note that as one selects a unit cell, the generated reflections for that cell are shown in the plot with dashed red lines. Sliding the cursor over these lines shows a small popup window with the indexed hkl for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å generates very many lines with no corresponding peaks (NB: this solution might not always show up!)

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Step 8. Select/Refine Cell

dashed red lines to solid blue ones). Import the cell information using the Cell Index/Refine/Copy Cell menu option. Then optimize the cell by refining the lattice parameters and the two-theta zero: click on the Refine? checkbox next to the Zero offset value and then mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Cell Index/Refine/Copy Cell menu option. Then optimize the cell by refining the lattice parameters and the two-theta zero: click on the Cell Index/Refine/Refine Cell menu option. The M20 improves to ~3600 and the a cell parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The certificate value for NIST SRM 660a is 4.15692 Å). Press the Show hkl mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine? checkbox next to the Zero offset value and then the Cell Index/Refine/Refine Cell menu option. The M20 improves to ~3600 and the a cell parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The certificate value for NIST SRM 660a is 4.15692 Å). Press the Show hkl positions button to update the plot including the refined Zero offset (in this case hardly anything happens!).

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Zero offset (in this case hardly anything happens!).

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Notice that a new entry heads the list in the Indexing Result section of the Unit Cells List window with an improved M20(~3600) and a new value for Zero offset is shown. NB: the Indexing Result section of the Show hkl positions button has an additional use; you can enter the Bravais lattice, Space group & Unit Cells List window with an improved M20(~3600) and a new value for Zero offset is shown. NB: the Show hkl positions button has an additional use; you can enter the Bravais lattice, Space group & Unit cell for any material. Then pressing (Optional) Finally, use of the Cell Index/Refine/Make new phase menu option allows one to create a phase with these lattice parameters in the data tree under Phases.Cell Index/Refine/Make new phase menu option allows one to create a phase with these lattice parameters in the data tree under Phases.  A name for the new phase is requested. This creates the tree item Phases (if it wasnt already present). This new phase can be used in future analysis (e.g. Rietveld or Pawley refinement).

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases (if it wasnt already present). This new phase can be used in future analysis (e.g. Rietveld or Pawley refinement).

To continue with the second part of this exercise, select the menu item File/New project in the File/New project in the GSAS-II data tree window. You will be asked if you want the current project saved; if Yes then all the peak fitting/indexing & cell refinement results will be saved to the Yes then all the peak fitting/indexing & cell refinement results will be saved to the LaB6.gpx file. If No then the file will remain as it was when created at Step 4 above.

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No then the file will remain as it was when created at Step 4 above.

2nd Fit Peaks/In this exercise we will fit peaks and index them for the new mineral jadarite (aka jadarite (aka kryptonite). The data were also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more

The file is FitPeaks\data\11bmb_6231.fxye; it has a corresponding prm file. Load them in & the plot is

minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks
\data\11bmb_6231.fxye; it has a corresponding prm file. Load them in & the plot is

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Ive zoomed in & shifted the plot some to highlight the

Set the limits as 3 and 9.

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3 and 9. This will give a suitable number of lines for indexing.

Step 3 Pick peaks

above, refine the peaks and the profile shape parameters in Instrument Parameters. You will be asked for a project file name at the first refinement (I used jadarite). In the end my refinement converged at Rwp=11.41% and some peaks do show some discrepancy as the sample is more complex than the simple U, V, W, X, Y model can accommodate. Make sure no peaks drift away during refinement (one weak one at ~6.67 is particularly troublesome). However, this is good enough to proceed.

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Instrument Parameters. You will be asked for a project file name at the first refinement (I used jadarite). In the end my refinement converged at Rwp=11.41% and some peaks do show some discrepancy as the sample is more complex than the simple U, V, W, X, Y model can accommodate. Make sure no peaks drift away during refinement (one weak one at ~6.67 is particularly troublesome). However, this is good enough to proceed.

Step 5. Prepare Indexing Peak List

Step 6. Index the cell

Lets assume that we know the cell is primitive monoclinic. In a real world case we wouldnt know this and we would have to try each Lets assume that we know the cell is primitive monoclinic. In a real world case we wouldnt know this and we would have to try each Bravais lattice. These can be done as a group, but it takes time to go through all the bad cases.

Select Monoclinic-P and do Cell Index/Refine/Index cell in the Unit Cells List window. Progress will be much slower and suitable results will be slow in coming so be patient. Watch the console window; the right answer will have an obviously large M20 (~380) and a volume of ~594Å3 (10th column of console display). Once this is seen (it may take more than one try to get this) you can stop the indexing search by pressing Cancel on the progress bar window. Notice the keep column; this allows you to keep some solutions from one indexing run to the next. It may take more than one press to fully stop it. My result was

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P and do Cell Index/Refine/Index cell in the Unit Cells List window. Progress will be much slower and suitable results will be slow in coming so be patient. Watch the console window; the right answer will have an obviously large M20 (~380) and a volume of ~594Å3 (10th column of console display). Once this is seen (it may take more than one try to get this) you can stop the indexing search by pressing Cancel on the progress bar window. Notice the keep column; this allows you to keep some solutions from one indexing run to the next. It may take more than one press to fully stop it. My result was

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Notice there may be other equally good M20 results with indexing. Be sure to use Keep to keep good ones as you try new indexing runs. The best solution is the one with the smaller volume and β > 90 deg. The plot shows every peak indexed including a weak peak not mso-hansi-theme-font:minor-latin'>Keep to keep good ones as you try new indexing runs. The best solution is the one with the smaller volume and β > 90 deg. The plot shows every peak indexed including a weak peak not selected for the peak fitting, although the weak peak at 21/n. Armed with this information you can Make new phase for the indexed cell (I called it Make new phase for the indexed cell (I called it kryptonite) and select

Notice that the lattice parameters and space group have been set for you. If you set the space group here a dialog box will appear.

This concludes this exercise; Save the project file as it is needed for the Charge set for you.

This concludes this exercise; do Save project as it is needed for the Charge Flipping in GSAS exercise. The features of the Phase Data window will be presented in other exercises.

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Phase Data
window will be presented in other exercises.

3rd Fit Peaks/Autoindexing in GSAS-II

In this exercise we will fit peaks and index them for sucrose in preparation for a charge flipping exercise. If continuing from the previous indexing example do In this exercise we will fit peaks and index them for sucrose in preparation for a charge flipping exercise. If continuing from the previous indexing example do File/New project from the main mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font: minor-latin'>11bmb_8714.fxye,  11bmb_8716.fxye 11bmb_8716.fxye and the corresponding .prm files.

The file is FitPeaksFitPeaks\data\11bmb_8716.fxye; it has a corresponding prm file and is for Domino® sugar ground under acetone. The other fxye file in this directory 11bmb_8714.fxye is for Domino® 10X powdered sugar used as is out of the box. Load the \data\11bmb_8716.fxye; it has a corresponding prm file and is for Domino® sugar ground under acetone. The other fxye file in this directory 11bmb_8714.fxye is for Domino® 10X powdered sugar used as is out of the box. Load the 8716 file in & the plot is

minor-latin;mso-hansi-theme-font:minor-latin'>8716 file in & the plot is

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Ive zoomed in & shifted the plot some to highlight the

Set the limits as 2 and 8.

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>2 and 8. Again, this gives a reasonable number of peaks for indexing.

Step 3 Pick peaks

kryptonite examples above, refine the peaks and the profile shape parameters in Instrument Parameters. You will be asked for a project file name at the first refinement (I used sucrose). In the end my refinement converged at Rwp=6.69% and some peaks do show some discrepancy as the sample is more complex than the simple U, V, W, X, Y model can accommodate. Make sure no peaks drift away during refinement. However, this is good enough to proceed.

mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: minor-latin'>Instrument Parameters. You will be asked for a project file name at the first refinement (I used sucrose). In the end my refinement converged at Rwp=6.69% and some peaks do show some discrepancy as the sample is more complex than the simple U, V, W, X, Y model can accommodate. Make sure no peaks drift away during refinement. However, this is good enough to proceed.

Step 5. Prepare Indexing Peak List

Step 6. Index the cell

Select Monoclinic-P and do Cell Index/Refine/Index cell in the Unit Cells List window. Progress will be much slower than for LaB6 but oddly much faster than for kryptonite and suitable results may appear almost immediately. Watch the console window; the right answer will have an obviously large M20 (~900) and a volume of ~704Å3 (10th column of console display). Once this is seen (it may take more than one try to get this) you can stop the indexing search by pressing Monoclinic-P and do Cell Index/Refine/Index cell in the Unit Cells List window. Progress will be much slower than for LaB6 but oddly much faster than for kryptonite and suitable results may appear almost immediately. Watch the console window; the right answer will have an obviously large M20 (~900) and a volume of ~704Å3 (10th column of console display). Once this is seen (it may take more than one try to get this) you can stop the indexing search by pressing Cancel on the progress bar window. Notice the keep column; this allows you to keep

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Notice there may be other equally good M20 results with mso-hansi-theme-font:minor-latin'>Keep to keep good ones as you try new indexing runs. The best solution is the one with the smaller volume and β > 90 deg. The plot shows every peak indexed including the weak peaks not selected for the peak fitting. Copy the best cell and try to refine it along with the Zero offset. I obtained an improved M20 ~1300 and slightly different lattice parameters. Try Armed with this information you can Make new phase for the indexed cell (I called it sucrose) and select Phases/sucrose from the GSAS-II data tree.

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new phase for the indexed cell (I called it sucrose) and select Phases/sucrose from the GSAS-II data tree.

set for you. This concludes this exercise; Save the project file as it is needed for the sucrose Charge Flipping exercise. The features of the Phase Data window will be presented in other exercises.

mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save the project file as it is needed for the sucrose Charge Flipping exercise. The features of the Phase Data window will be presented in other exercises.

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