Description: GSAS-II logoHelp for GSAS-II – Powder Diffraction Tree Items

This is where to find help on the Tree item in GSAS-II associated with powder diffraction (labeled PWDR) and its associated subitems.

PWDR Help Index

6A. Powder histogram (PWDR) Data Tree headings



6A. Powder Histograms - type PWDR

When a powder diffraction dataset (prefix ‘PWDR’) is selected from the data tree the dataset is plotted. The observed data points are shown as blue crosses and where fit, the calculated pattern is shown as a green line; the background is shown as red line. The difference curve is shown as a cyan line. Reflection positions are shown with small vertical lines.

Each powder diffraction dataset has a number of children in the tree as are shown below. Clicking on any of them produces changes in the plot and allows access to different parameters associated with the dataset.

·       Comments

·       Limits

·       Background

·       Instrument Parameters

·       Sample Parameters

·       Peak List

·       Index Peak List

·       Unit Cells List

·       Reflection Lists

What can I do here?

Menu Commands

a.     a. Error Analysis – this produces a ‘normal probability’ plot for the refinement result as bounded by the limits. The slope and intercept of the curve in the central region (-1 < / < 1) are shown on the plot status line. The slope is the square root of GOF for the best fit set of data points (~68% of the data).

What is plotted here?

The powder patterns that are part of your project are shown on this page. They can be displayed as a stack of powder patterns, just a single pattern or as a contour image of the peak intensities. What can be done here will depend on home many patterns are shown as well as what mode is selected. Note that the tick marks and difference curve positions can be customized, as discussed below.

Similar plots to the one here are displayed when different subtree items are selected and on those plots it is possible to view and in some cases edit information associated with the histogram. As examples:

·       By selecting the Limits entry, range of data used, as well as possible excluded regions, can be set.

·       Selecting Reflection Lists allows display of reflection indicies (hkl values) for a selected phase. Letting the mouse rest unmoved at the position of a reflection in 2-theta, Q, etc. (the vertical position does not matter) will cause these to be displayed. After a short delay a "tool tip" will appear with indicies for any reflections close to the lateral mouse position.

·       Selecting Background allows a mouse to be used to define fixed points where a background curve can be fitted to those points.

·       Selecting Instrument Parametersdisplays plot of peak widths as a function of 2theta or Q.

·       Selecting Peak List allows postions of peaks to be defined for use in direct peak fitting.

·       Selecting Unit Cells List can show the positions of reflections for an arbitrary set of unit cell parameters, optionally with space group extinctions applied.

What can I do with the plot?

Move mouse

As the mouse cursor is moved across the plot, the plot status line will show the cursor position as 2Theta, d-spacing and the intensity. For a Q-plot, Q is shown instead of 2Theta.

Press keyboard keys

See below. The "s" and "w" modes are commonly used.

Drag tickmarks

Click on any tick mark and while holding the left mouse button down move them to where you want them to be displayed (press the s key for Sqrt(I) mode to reset to the defaults). With multiple phases, clicking on the 2nd phase, etc. changes the vertical spacing between phases. Tick marks can be dragged only when the main PWDR or Reflection Lists tree items are selected.

Drag the difference curve

When the "normal" obs-calc plot is shown (as opposed to the preferred "w" mode plot where (obs-calc)/sigma is displayed, click on any point in the difference curve and while holding the left mouse button down move the curve to where you want it to be displayed (press the s key for Sqrt(I) mode to reset it to the default). The difference curve can be dragged only when the main PWDR or Reflection Lists tree items are selected.

Display/edit histogram information

By selecting different tree items within the current histogram, it is possible to display and in some cases edit information associated with the histogram. See above.

Create a Publication-ready plot

Press the green "P" button to generate a customizable version of the displayed plot that can be exported at high resolution.

The following key press characters are defined (not for all plot modes). These actions can also be initiated from the Key Press button on the plot toolbar.

For line plots:

s: Sqrt(I) on/off

changes the y-axis to be the square-root of the intensity. The tick mark and the difference curve location is reset.

w: toggle diff plot mode

for the pattern selected from the data tree, this will replace the difference (obs-calc) curve with the differences divided by their standard uncertainty (esd) values [(obs-calc)/sigma], which shows the significance of the deviations in the fit of the pattern. (Recommended).

b: subtract background

Subtracts the fitted background from the powder pattern. Pressing this again turns the mode off.

n: log(I) on/off

changes the y-axis to be the log10 of the intensity; difference curve is not shown for log(I) on.

q: toggle Q plot

changes the x-axis from 2Theta to Q. This will put multiple powder patterns taken at different wavelengths/types on the same x-axis scale.

t: toggle D-space plot

changes the x-axis from 2Theta to d-space. This will put multiple powder patterns taken at different wavelengths/types on the same x-axis scale. May not be very useful with data over a wide range.

e: set excluded region

Defines a new excluded region: press the "e" key with the mouse on one side of the region. Move the mouse to the other side and and press "e" again. The region markers (magenta dashed lines) can be dragged to new positions. Available only when the Limits tree entry is selected.

x: show excluded region

Normally all observed data is plotted. When the "x" key is pressed, data inside excluded regions are not shown.

.: scaling diagnostic

When the '.' key is pressed, data are plotted where the intensity scale shows the equivalent number of counts so that uncertainty on each point is the sqrt(I).

g: grid lines

Draws vertical and horizontal grid lines at all axis label positions.

a: add magnification region

Adds a magnification region to the plot and sets the magnification amount to x2. This can be edited (or deleted) in the table that is shown when the main PWDR tree entry is selected.

For line plots with more than one powder pattern:

c: contour on/off

if multiple powder profiles, then a contour plot is shown of the observed intensities. All data sets must be the same length as the first one to be included in the contour plot.

S: set color Scheme

Select the color map used for contour plots

m: toggle single/multiple plot

for multiple powder profiles, this will show only the one selected from the data tree. The offset options (below) are not active.

f: select data

Allows only some powder patterns to be plotted, rather than all.

+,=: no selection

for multiple powder profiles, only the observed curve is shown when this mode is turned on ('+' and '=' do exactly the same thing).

/: normalize

for multiple powder profiles, all diffraction datasets are normalized so that the maximum intensity is 1.

Offset modes for line plots in waterfall mode (multiple patterns only):

l: offset left

for a waterfall plot of multiple powder profiles, increase the offset so that later plots are shifted more to the left relative to previous plots.

r: offset right

for a waterfall plot of multiple powder profiles, increase the offset to the right (or decrease the left offset.)

d,D: offset down

for a waterfall plot of multiple powder profiles, increase the offset down. (D does the same as d but to a much larger amount)

u,U: offset up

for a waterfall plot of multiple powder profiles, increase the offset up. (U does the same as u but to a much larger amount)

o: reset offset

for a waterfall plot of multiple powder profiles, reset to no offset.

For contour plots:

d: lower contour max

this lowers the level chosen for the highest contour color.

u: raise contour max

this raises the level chosen for the highest contour color

i: interpolation method

this changes the method used to represent the contours. If selected a dialog box appears with all the possible choices. Default is ‘nearest’; the other useful choice is ‘bilinear’, this will smooth out the contours.

s: color scheme

this changes the color scheme for the contouring. Default is ‘Paired’, black/ white options are ‘Greys’ and ‘binary’ (for black on white) or ‘gray’ (for white on black). Others can be very colorful (but not useful!)

c: contour off/on

this turns off contouring and returns to a waterfall plot with any offsets applied.

For display of reflections from magnetic unit space groups

j: show next; reset use flag

Show the next magnetic space group in the list, clearing the "Use" flag for the currently displayed space group. (available from Index Unit Cells only).

k: show next

Show the next magnetic space group in the list. The "Use" flag for the currently displayed space group is unchanged. (available from Index Unit Cells only).

Comments

This window shows whatever comment lines (preceded by “#”) found when the powder data file was read by GSAS-II. If you are lucky, there will be useful information here (e.g. sample name, date collected, wavelength used, etc.). If not, this window will be blank. The text is read-only.

Limits

This window shows the limits in position to be used in any fitting for this powder pattern. The ‘original’ values are obtained from the minimum & maximum values in the powder pattern. The ‘new’ values determine the range of data that will be used in fitting. Units are 2Theta for CW data and time (microsec) for TOF data.

What can I do here?

You can change the "new" values for Tmin and Tmax as needed. Change the upper and lower Tmin values by clicking on the appropriate vertical line and dragging it to the right or left or by typing values into the data window.

Menu ‘Edit Limits

Copy

this copies the limits shown to other selected powder patterns. If used, a dialog box (Copy Parameters) will appear showing the list of available powder patterns, you can copy the limits parameters to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation.

Add Exclude

Select this menu item and click on a data point. A pair of magenta lines is drawn to indicate a range that should be excluded. (No green solid line with the computed pattern is shown for those data). The magenta lines can be dragged, as described below for setting data limits.

What is plotted here?

The plot is the same as for Powder Histograms - type PWDR and the key press commands are all the same. However, two vertical lines are displayed, green for the lower Tmin value and red for the upper Tmin value. These can be dragged to set limits.

What can I do with the plot?

The upper and lower Tmin values can be changed by clicking on the appropriate vertical line and dragging it to the right or left.

Background

This window shows the choice of background functions and coefficients to be used in fitting this powder pattern. There are three types of contributions available for the background:

1). A continuous empirical function (‘chebyschev’, ‘chebyschev-1’, ‘cosine’, ‘lin interpolate’, ‘inv interpolate’ & ‘log interpolate’). The latter three select fixed points with spacing that is equal, inversely equal or equal on a log scale of the x-coordinate. The set of magnitudes at each point then comprise the background variables. All are refined when refine is selected. Note that ‘chebyschev-1' is a better choice than ‘chebyschev’.

2). A set of Debye diffuse scattering equation terms of the form:

where A,R & U are the possible variables and can be individually selected as desired; Q = 2π/d.

3). A set of individual Bragg peaks using the pseudo-Voigt profile function as their shapes. Their parameters are ‘pos’, ’int’, ‘sig’ & ‘gam’; each can be selected for refinement. The default values for sig & gam (=0.10) are for very sharp peaks, you may adjust them accordingly to the kind of peak you are trying to fit before trying to refine them.

What can I do here?

1.     Menu ‘Background’ –

a.     Copy – this copies the background parameters shown to other selected powder patterns. If used, a dialog box (Copy Parameters) will appear showing the list of available powder patterns, you can copy the background parameters to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation.

b.     Copy flags – this copies only the refinement flags shown to other selected powder patterns. If used, a dialog box (Copy Refinement Flags) will appear showing the list of available powder patterns, you can copy the refinement flags to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation.

2.     You can select a different Background function from the pull down tab.

3.     You can choose to refine/not refine the background coefficients.

4.     You can select the number of background coefficients to be used (1-36).

5.     You can change individual background coefficient values. Enter the value then press Enter or click the mouse elsewhere in the Background window. This will set the new value.

6.     You can introduce one or more Debye scattering terms into the background. For each one you should enter a sensible value for ‘R’ – an expected interatomic distance in an amorphous phase is appropriate. Select parameters to refine; usually start with the ‘A’ coefficients.

7.     You can introduce single Bragg peaks into the background. For each you should specify at least the position. Select parameters to refine; usually start with the ‘int’ coefficients.

What is plotted here?

The plot is the same as for Powder Histograms - type PWDR and the key press commands are largerly the same. Specific to this plot are fixed background points. These can be added, deleted and moved. Once that is done the background parameters for the selected function can be fitted to the fixed points.

Instrument Parameters

This window shows the instrument parameters for the selected powder data set. The plot window shows the corresponding resolution curves. Solid lines are for the default values (in parentheses), dashed lines from the refined values and ‘+’ for individual entries in the ‘Peak_List’.

What can I do here?

1.     Menu ‘Operations’ –

a.     Load profile… - loads a GSAS-II instrument parameter file (name.instprm), replacing the existing instrument parameter values. All refinement flags are unset.

b.     Save profile… - saves the current instrument parameter values in a simple text file (name.instprm); you will be prompted for the file name – do not change the extension. This file may be edited but heed the warning to not change the parameter names, the order of the parameter records or add new parameter records as this will invalidate the file. You may only change the numeric values if necessary. You can change or add comment records (begins with ‘#’).

c.     Reset profile – resets the values for the instrument parameters to the default values shown in parentheses for each entry.

d.     Copy – this copies the instrument parameters shown to other selected powder patterns. If used, a dialog box (Copy parameters) will appear showing the list of available powder patterns, you can copy the instrument parameters to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation. The copy will only work for instrument parameters that are commensurate with the one that is shown, e.g. single radiation patterns will not be updated from Ka1/Ka2 ones.

e.     Copy flags - – this copies the instrument parameter refinement flags shown to other selected powder patterns. If used, a dialog box (Copy refinement flags) will appear showing the list of available powder patterns, you can copy the instrument parameter refinement flags to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation. The copy will only work for instrument parameters that are commensurate with the one that is shown, e.g. single radiation patterns will not be updated from Ka1/Ka2 ones.

2.     You can change any of the profile coefficients

3.     You can choose to refine any profile coefficients. NB: In certain circumstances some choices are ignored e.g. Zero is not refined during peak fitting. Also some choices may lead to unstable refinement, e.g. Lam refinement and lattice parameter refinement. Examine the ‘Covariance’ display for highly correlated parameters.

What is plotted here?

This plot shows the contributions to the powder pattern peak widths as delta-Q/Q (=delta-d/d) vs. Q for the Gaussian and Lorentzian parts of the profile function, in addition to the overall widths. The solid curves are based on the default values of U, V, W, X and Y shown in the Instrument Parameters window (shown in parentheses; these are the values for the instrument contribution that were set when the powder pattern was first read in to GSAS-II.) The dashed values are based on the refined values, if different. If individual peak fitting has been performed, the values of ‘sig’ & ‘gam’ for those peaks are plotted as ‘+’; these are computed from the fitted values of U, V, W, X and Y as well as any sig or gam values that are individually refined.

Sample Parameters

This window shows the various sample-dependent parameters for the selected powder pattern. The presence of a refine button indicates that a parameter can be refined (all others are fixed.) All values shown in this window can be edited. Note that the last three parameters (named FreePrmX, X=1,2,3) have labels that can be changed. If changed in one histogram, the same label is used for all histograms. When a label is changed, the Comments tree item for each PWDR histogram is searched for a matching "Label=value" pair (differences in letter case between the two label strings is ignored). When found, the value is converted to a float and saved as the appropriate Sample Parameter. NB: for powder data be sure the correct instrument type is selected (Debye-Scherrer or Bragg-Brentano).

What can I do here?

Command Menu items

In this window you can change parameters associated with a histogram or set them to be refined. The histogram scale factor is usually refined. For Debye-Scherrer mode the "Sample X displacement" is also ususally refined but the "Sample Y displacement" can only be refined when data are collected over a two-theta range that extends to greater than ~140 degrees (typically for CW Neutron). Sample absorption should not be refined when all atomic displacement parameters (Uiso or Uaniso values) are varied, as the correlation is very high. For Bragg-Brentano, "Sample displacement" is usually refined and for low-Z samples "Sample transparency" is usually refined. "Surface roughness" parameters are not usually refined. Remaining parameters are of use for texture or parametric studies and may be changed with the menu commands described here.

Set scale

Rescales a pattern by multiplying by the current scale factor.

Load

This loads sample parameters from a previously saved .samprm file.

Save

This saves the sample parameters to a file with the extension ’.samprm’. A file dialog box will appear to ask for the name of the file to be written.

Copy

This copies the sample parameters shown to other selected powder patterns. If used, a dialog box (Copy parameters) will appear showing the list of available powder patterns, you can copy the sample parameters to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation.

Copy selected...

This copies only the sample parameter that are selected to other selected powder patterns, but is otherwise similar to "Copy".

Copy flags

This copies the sample parameter refinement flags shown to other selected powder patterns. If used, a dialog box (Copy refinement flags) will appear showing the list of available powder patterns, you can copy the sample parameter refinement flags to any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation.

Set one value

This is used to set a single selected sample parameter for a selected set of PWDR histograms. The same value can be used for all histograms or a dialog can be used to provide a table where you can set the values differently for each of selected histograms.

Load all

Reads a file containing a table of sample parameters and copies them to matching PWDR entries. The file will look something like the example here:

 
#filename       temperature pressure ignore-me  humidity
LaB6_dc250.tif      100          1      test       .2
LaB6_dc300.tif      150          1      test       .25

Note that the first line(s) in the file can be a header, but each header line must start marked with a hash (#). A header is not required. "Columns" in the table are separated by one or more delimiters (which may be a comma, tab or space). Note that columns do not need to be aligned, as long as each entry is spaced by at least one delimiter. The first column in the table is used to look up PWDR entries where the initial space-delimited string after the PWDR tag ("myfile" in "PWRD myfile AZM=180...") must match the table. Subsequent columns can then be mapped to sample parameters or can be ignored, using a dialog window.

Rescale all

Allows a series of selected PWDR histograms to be put on a common scale by integrating them over a specific two-theta region and then scaling them so that the integration range will match the first pattern.

Peak List

The Peak List data tree entry is used to fit diffraction peaks at user-supplied positions (not generated from a unit cell). Peak positions and intensities may be selected for individual refinement. Gaussian (sigma) and Lorentzian (gamma) peak widths may be varied individually or the values may be generated from the U,V & W (sigma) and X & Y (gamma) values in the Instrument Parameters tree item: If individual values are refined, then the value in the table is used. If values are not refined, then those determined by U,V & W and/or X & Y are placed in the table and are used. Likewise, the background is generated using the parameters in the Background data tree entry and the range of data used in the fit is set from the Limits tree item. Note that optionally the parameters on the Background and in the Instrument Parameters tree items may be refined as peak settings are fitted.

What can I do here?

There are three ways to interact with Peak List data tree item: through its menu, labeled Peak Fitting, through interaction with the peak list table, and through interactions with the plot.

The following interactions are available with the peak table:

·  You can change individual peak coefficient values. Enter the value then press Enter or Tab or click the mouse elsewhere in the Peak List window. This will set the new value.

·  You can change the individual refine flags either by clicking on the check boxes.

·  You can change all refine flags in a column by clicking on a single one and then click on the column label above. The entire column should be highlighted in blue. Type ‘y’ to set the refine flags or ‘n’ to clear the flags. This can also be done by double-clicking on the column label, which brings up a menu.

·  You can delete peaks in the Peak List by selecting a row by clicking on the row label to the left (multiple selection of rows is allowed). Selected rows will be highlighted in the plot (see below). Then press the Delete or backspace key. (Note that peaks can also be deleted from the plot, see below.)

·  You can highlight a peak by clicking or double-clicking on the row label (to the left) for a peak. The color of the line will change from blue to green.

The Peak Fitting menu contains the following commands:

Set sel. ref flags

If one or more row of peaks are selected by clicking on the peak label to the left, this menu item can be used to set the refinement flags for the selected reflections.

Set all ref flags

This sets refinement flags for all peaks in the table.

Auto search

This fills the table with peak positions. These are selected based on peak tops that are substantially above background. Noisy data will give spurious peaks and small peaks or shoulders will not be found. Examine results & modify as needed.

UnDo

Resets peak parameters, background and instrument parameter values varied in the last peak fitting refinement back to their original values. Use this to recover from a failed refinement. Note: only one previous refinement is saved, so this cannot be pressed twice to return to the refinement before the previous.

PeakFit

Performs a least squares fit of the peaks in Peak List to the data. Any peak parameters, background parameters and instrument parameters with refine checked will be varied in this refinement. The refinement will proceed until convergence. We suggest you vary the intensity along with the background first (the default), then vary the position and instrument parameters after. The order will depend on how poor is the initial estimate of the instrument parameters (U, V, W, X, Y & SH/L). To determine how to proceed, examine in detail the powder pattern difference curve displayed in the GSASII Plots window. If individual peaks show peak widths that are widely different, their individual sigma and gamma parameters may be refined. If the refinement results in negative peak coefficients, these will be highlighted in red. If this happens, you should use the UnDo menu item (above) to return to the refinement and reconsider your choice of parameters to be varied.

LSQ one cycle

Perform a single cycle of least squares refinement. This can be used in difficult cases to get a refinement started toward convergence.

Reset sig and gam

This resets the values of sigma and gamma in the table to those computed from the instrument parameters U, V, W, X & Y.

Peak copy

Copy the current set of peaks to other histogram(s)

Seq PeakFit

Fit peaks for multiple histograms

Clear peaks

This removes all the peaks from the Peak List.

Move selected peak

A peak may be moved using the following process: select it in the table by clicking on its label (to left), use this menu item. The peak line will then follow movement of the mouse in the plot window. Click with the left mouse button to set a new position. Click with the right mouse button to delete that peak. Click outside the axes to abort the move and return to the previous position. (Note that peak movement is also possible with the plot window, see below.)

What is plotted here?

The plot window shows the observed and computed patterns, as well as the background and peak positions. Observed points are shown as blue crosses (+) and the fitted pattern is shown as a solid green line. The background is shown as a red line and the difference curve is shown as a cyan (turquoise) line, below the observed and computed pattern. Peak positions are shown as vertical blue lines (or green when selected). The upper and lower data limits are shown as red and green dashed vertical lines, respectively.

What can I do with the plot?

For all actions involving mouse clicks such as those below, be sure that the Zoom/Pan buttons are not selected on the Plot window, as the mouse clicks will be used for zooming or panning, not the desired action.

·  You can add peaks to the Peak list using the mouse on the plot by: position the cursor pointer onto a cross for an observed point and pressing the left mouse button. The selected peak will be added to the Peak List in the appropriate position to keep peaks sorted and a blue vertical line will be plotted on that position. We recommend that you begin picking peaks from the right side of the pattern; that way the tool tip won’t be in your way as you select peaks.

·  You can delete peaks using the mouse on the plot by positioning the pointer on the blue line for the peak to be deleted and then pressing the right mouse button. The blue line should vanish and the corresponding peak will be removed from the Peak List.

·  You can move a Peak List item using the mouse on the plot by: position the pointer on the blue line for the peak you wish to move and then hold the left mouse button down, dragging the line to the desired position. When the mouse button is released, the peak line will be drawn in the new position.

·  The fit limits can be changed without selecting the Limits item in the data tree from the plot. Change the upper and lower Tmin values by clicking on the appropriate vertical line and dragging it to the right or left.

Index Peak List

This window shows the list of peaks that will be used for indexing (see Unit Cells List). It must be filled before indexing can proceed. When indexing is completed, this display will show the resulting hkl values for every indexed reflection along with the calculated d-spacing (‘d-calc’) for the selected unit cell in Unit Cells List. .

What can I do here?

1. Menu ‘Operations’ – Load/Reload – loads the peak positions & intensities from the Peak List to make them available for the indexing routine. The d-obs is obtained from Bragg’s Law after applying the Zero correction shown on the Instrument Parameters table to the position shown here.

2. You may deselect individual peaks from indexing by unchecking the corresponding ‘use’ box.

Unit Cells List

This tree item has several purposes, it can be used to perform autoindexing and it can be used to show the positions of peaks from unit cells which may be results from autoindexing or may be entered from a phase or manually. It can be used to refine unit cell parameters. It can also be used to search for cells/symmetry settings related to a specified unit cell & space group.

What can I do here?

For autoindexing, the peaks in the Index Peak List are used. Select one or more Bravais lattice types to use and use the "Cell Index/Refine"/"Index Cell" menu command to start indexing. Output will appear on the console and a progress bar dialog will appear which tracks trial volume. A Cancel button will terminate indexing; it may need to be pressed more than once to fully terminate the indexing process. Console output shows possible solutions with a computed M20 for each; good solutions are indicated by high M20 values. X20 gives number of unindexed lines out of the 1st 20 lines and Nc gives total number of reflections generated for each solution.

The "Copy Cell" menu commnd copies a selected solution to the Unit cell values; the Bravais lattice shown for the choice is copied. Press Show hkl positions to generate the allowed reflection positions, which are visually superimposed on the displayed powder pattern to visually confirm the indexing. Pay particular attention to any unmatched peaks in the pattern. A Space group can be from the pulldown box to remove reflections based on space group extinctions and visually eliminate possiblities.

1.     Max Nc/Nobs: – this controls the extent of the search for the correct indexing. This may need to be increased if an indexing trial terminates too quickly. It rarely needs to be changed.

2.     Start Volume: – this sets an initial unit cell volume for the indexing. It rarely needs to be changed.

3.     Select "keep" in the table for a cell that should be preserved when an additional indexing run is tried; all without that are erased before the indexing trial begins.

To display a unit cell, optionally with space group extinctions, set a Bravais class to determine a unit cell type (see list below), optionally select a space group (by default the lowest symmetry space group for the class is selected) and enter the unit cell contents. Or use the "Cell Index/Refine"/"Load Phase" menu command to read this information from a phase that has been read into a project or from a file (such as a CIF) using the "Cell Index/Refine"/"Import Cell" menu command.

For symmetry exploration, once a phase/cell has been loaded, use the "Run SUBGROUPS", "Cell Symmetry Search" or "Run k-SUBGROUPSMAG" commands from the "Cell Index/Refine" menu. These commands look for: subgroups, higher symmetry cells or magnetic subgroups, respectively. Also note the "Transform Cell" commnd in that menu that can perform namy common lattice transformations, apply a user-supplied cell transformation or create a magnetic phase.

To optimize a cell, to fit the peaks in the Index Peak List, use the "Cell Index/Refine"/"Refine Cell" menu command. The results will be placed in the Indexing Result table with ‘use’ selected.

Other: The "Make new phase" command creates a new phase from the selected unit cell and chosen space group. A dialog box will appear asking for a name for this phase. See the new entry under Phases and the new lattice parameters will be in the General window for that phase.

GSAS-II Laue classes (note that some redundant entries are included for convenience.)

·   Cubic: Fm3m, Im3m & Pm3m

·   Rhombohedral: R3-H (hexagonal axes)

·   Hexagonal: P6/mmm

·   Tetragonal: I4/mmm, P4/mmm

·   Orthorhombic: Fmmm, Immm, Ammm, Bmmm, Cmmm, Pmmm

·   Monoclinic: I2/m, C2/m, P2/m (b-unique)

·   Triclinic: P1, C1

Reflection Lists

This window shows the reflections for the selected phase (selected by the tab at top) found in this powder data set. It is generated by a Rietveld (including Pawley and LeBail) refinements. Reflection d-spaces are generated directly from lattice parameters but 2θ values will incorporate corrections, such as for sample displacement, zero, etc.

The indicies (hkl values) for reflections can be displayed by letting the mouse rest at the position of a reflection in 2-theta, Q, etc. (the vertical position does not matter). After a short delay, a "tool tip" will be displayed for any reflections close to the lateral mouse position.

What can I do here?

1. Menu ‘Reflection List’

a.     Select phase – if there is more than one phase; you can select another phase; the window title will show which phase is shown.



Last modified: Tue Apr 27 22:21:15 CDT 2021