Help for GSAS-II
This
is where to find help on various GSAS-II windows and plots. Note that GSAS-II
operates with three windows: the main GSAS-II data tree
section, which provides a hierarchical view of the current project on
the left and the GSAS-II data editing section, which shows the contents of
a particular section of the project, where values can be examined and changed;
The second is the GSAS-II Plots window, which shows graphical
representations of the results. The third is a console window, which has printout information
that can be selected, cut & pasted into a document.
Help Index
- Learning GSAS-II: tutorials
- Application windows
- Main menu commands
- Data Tree headings, graphics windows and menu commands
- Top-level Data Tree headings
- Phase Data Tree headings
- Image (IMG) Data Tree headings
- Powder histogram (PWDR) Data Tree headings
- Single Crystal histogram (HKLF) Data Tree headings
- Pair Distribution Functions (PDF) Data Tree headings
- Powder Peaks (PKS) Data Tree headings
- Small Angle Scattering (SASD) Data Tree headings
- Other: Macintosh notes, Configuration options and Programmers documentation
Learning GSAS-II: Tutorials
The
best way to learn about how different sections of GSAS-II is used is
to work through tutorials. A list of available tutorial topics appears on a
separate web page.
The data tree shows contents of a GSAS-II project
(which can be read or saved as a .gpx file) in a hierarchical view.
Clicking on any item in the tree opens that information on the right
side of the window in the "Data Editing" section,
where information in that item can be viewed or edited. For example, the "Sample Parameters" item under a ‘PWDR’
entry contains information about how data were collected, such as the sample
temperature (see below). The arrow keys (up
& down) move the selection to successive entries in the data tree; both the
data window and the associated plot (if any) will change.
The leftmost entries in the GSAS-II menu provide access to many
features of GSAS-II. Other menu items will change depending on what
type of entry is selected in the data tree. The menu commands that
do not change and are described below in the
main menu commands section. Different information is displayed in the Data Editing
Window, depending on which section of the data tree is
selected. For example, clicking on the "Notebook" entry of the tree
brings up the Notebook editing window, as described below in the
data tree sections.
This window presents all the
graphical material as a multipage tabbed set of plots utilizing the matplotlib
python package. Each page has a tool with the
controls The first nine or ten
icons have the following functions: Home, Back, Forward, Pan, Zoom,
Resize plot,
Save, Key Press and Help, respectively and are
described below. The
remainder (yellow arrows) move or rescale the plot. Note that
Resize plot is removed from the toolbar where matplotlib
allows this and should not be used.
Below the toolbar may be a
status bar that on the left may show either an instruction for a keyed input or
a pull down selection of keyed input; on the right may be displayed position
dependent information that is updated as the mouse is moved over the plot
region. Note that as files are saved, copies of the previous version
are saved as backup files, named as {project}.bak{i}.gpx,
where i starts as 0 and is increased after each save
operation.
NB: you may open a backup .gpx file (e.g. name.bak3.gpx) to return
to a previous version of your project, but if you do so, it is
best to immediately use the
Note that for atom positions, the coordinate values (named as
‘p::Aw:n’, where p is the phase number, n is the atom number
and w is x, y or z) is
not a refinable parameter, but the shift in the value is. The
refined parameters are ‘p::Aw:n’.
The reason this is done is that by treating an atom
position as x+dx,y+dy,z+dz where the “d” values indicate shifts from
the starting position and the shifts
are refined rather than the x,y, or z values is that this simplifies
symmetry constraints. As an example, suppose we have an atom on
a symmetry constrained site, x,1/2-x,z. The process needed to define
this constraint, so
that if x moves positively y has to move negatively by the same
amount would be messy. With refinement of shifts, all we need to do is constrain dy (‘0::dAy:n’)
to be equal to -dx (-1*‘0::dAx:n’).
Press the window exit button to exit this dialog box.
GSAS-II uses separate routines to read in information from external
files that can be created and customized easily. See the GSAS-II
Import Modules section of the Programmers documentation for
more information on this. Since it is easy to support new formats,
the documentation below may not list all supported formats.
Note that it is possible to apply corrections to the 2-theta,
intensity or weight values by adding a Python command(s) to
the instrument (.instprm) parameter with a variable named
CorrectionCode. See the CorrectionCode.instprm.sample file
provided in the GSAS-II source directory for an example of how this
is done.
GSAS-II uses separate routines to write out files with
information inside GSAS-II. These routines can be
created and customized easily. See the GSAS-II Export Modules
section of the Programmers
documentation for more information on this. Since it is
easy to support new formats, the documentation below may not list
all supported formats.
This window provides a place for you to enter whatever text
commentary you wish. Each time you enter this window, a date/time entry is
provided for you. A possibly useful technique is to select a portion of the project.lst file after a refinement completes (it will
contain refinement results with residuals, new values & esds)
and paste it into this Notebook window so it becomes a part of your project
file.
Use the notebook to keep track of information related to how you use
GSAS-II. This window provides the main controls for the refinement
calculations in GSAS-II. Two of the main refinement tools are the fortran MINPACK lmdif and lmder algorithms wrapped in python as provided in the Scipy package and a third one is a python version utilizing
only the numpy package. The purpose is to minimize
the sum of the squares of M
nonlinear functions in N variables by a modification of the Levenberg-Marquardt
algorithm. The lmdif and lmder
routines were written by Burton S. Garbow,
Kenneth E. Hillstrom, Jorge J. More (Argonne National
Laboratory, 1980). The python/numpy version was developed by us based on the
material in Numerical Recipes (Press, Flannery, Teulosky
& Vetterling) for the Levenberg-Marquardt
algorithm and is the default. 1. Select whether the refinement
uses ‘analytic Jacobian’, ‘analytic Hessian’ or ‘numeric’ derivatives. The last
is slower and perhaps a bit less accurate, but may be needed if the analytic
functions are not fully developed. The Jacobian matrix is shaped N x M
(parameters x observations) and is much larger than the Hessian matrix which is
shaped M x M (parameters x parameters). Generally use ‘analytic Hessian’ for
routine work. 2. Select ‘Min delta-M/M’ for
convergence; the refinement will stop when the change in the minimization
function is less than this value. Set Min delta-M/M = 1.0 to force just a
single cycle to be performed. A value less than 10-4 (the default)
generally gives no better result. The allowed range is 10-9 to 1.0. 3. If ‘analytic Jacobean’ is
chosen then select ‘Initial shift factor’ for the first cycle of refinement.
This value is modified by the least squares routine. The allowed range is 10-5
to 100. Smaller values may be needed if your initial refinement trials
immediately diverge, however make sure your starting parameter values are
‘reasonable’. The selected default (=1.0) normally gives good performance. 4. If ‘analytic Hessian’ is
chosen then select ‘Max cycles’, the maximum number of least squares cycles to
be performed. Least squares cycles are determined by the number of times a new
Hessian matrix is computes; the Levenberg-Marquardt
algorithm may compute the function several times between cycles as it finds the
optimal value of the Marquardt coefficient. Choices are given in the pull down
selection; the default is 3 cycles. 5. Select data for sequential
refinement; the data sets may be done in ‘reverse order’.
This window contains final residual information; the GSASII
Plots window ‘Covariance’ shows a graphical
representation of the variance-covariance matrix. A text window is
displayed with statistical values and goodness of fit parameters.
The variance-covariance matrix as a color coded array is shown on this
page. The color bar to the right shows the range of covariances (-1 to
1) and corresponding colors. The parameter names are to the right and
the parameter numbers are below the plot.
Move the mouse cursor across the plot. If on a diagonal cell, the parameter name,
value and esd is shown both as a tool tip and in the right hand portion of the
status bar. If the cursor is off the diagonal, the two parameter names and
their covariance are shown in the tool tip and the status bar.
Use the Zoom and Pan buttons to focus on some
section of the variance-covariance matrix.
Press
‘s’ – A color scheme selection dialog is shown. Select a color scheme and press
OK, the new color scheme will be plotted. The default is ‘RdYlGn’.
Press ‘p’ – Saves the covariance values in a text file.
This window shows the constraints to be used in a
refinement. It is organized into three tabbed pages. ‘Phase constraints’ contain
those involving parameters that describe aspects of the crystalline phases to
be used in the refinement (e.g. atom coordinates, thermal motion and site
fraction parameters). ‘Histogram/Phase constraints’ are those which describe
aspects of the pattern that depend on both the phase and the data set used in
the refinement (e.g.
microstrain
and crystallite size parameters). ‘Histogram constraints’ are those that depend
only on the data set (e.g. profile coefficients U, V, W, X and Y).
1. Select the tab for the
parameter types you wish to constrain. Each will have the same possibilities in
the ‘Edit’ menu. 2. Menu ‘Edit’ – a. Add
Hold –
select a parameter that you wish to remain fixed although other parameters of
the same type may be selected as a group for refinement. For example, if the
space group for a phase has a polar axis (e.g. the b-axis in P21),
then one atom y-parameter is arbitrary and should be selected for a Hold to
keep the structure from drifting up or down the y-axis during refinement. If selected,
a dialog box will appear showing the list of available parameters; select one
and then OK to implement it, Cancel will cancel the operation. The held
parameter will be shown in the constraint window with the keyword ‘FIXED’. A
Delete button can be used to remove it. b. Add
equivalence
– select a list of parameters that should have the same value (possibly with a
non-unitary multiplier for some). Examples are a list of atoms with the same
thermal motion Uiso, sets of profile coefficients U,V,W across multiple data sets. If selected, a dialog box
will appear with a list of the available parameters. Select one and press OK; a
second dialog box will appear with only those parameters that can be made
equivalent to the first one. Choose those and press OK. Cancel in either dialog
will cancel the operation. The equivalenced parameters will show as an equation
of the form M1*P1+M2*P2=0; usually
M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword
‘EQUIV’ marks it as an equivalence. A Delete button can be used to remove it. c. Add
constraint –
select a list of parameters whose sum (with possible non-unitary multipliers)
is fixed. For example, the sum of site fractions for atoms on the same site
could be fixed to unity. If selected, a dialog box will appear with a list of
the available parameters. Select one and press OK; a second dialog box will
appear with only those parameters that can be used in a constraint with the
first one. Choose those and press OK. Cancel in either dialog will cancel the
operation. The equivalenced parameters will show as an equation of the form M1*P1+M2*P2+…=C;
the multipliers M1, M2, … and C can be changed via the ‘Edit’ button. The
keyword ‘CONSTR’ marks it as a constraint. A Delete button can be used to
remove it. d. Add
function –
this is very similar the “Add constraint” type except that the result of the
sum can be varied in the refinement. The keyword ‘FUNCT’ marks it as a
function; the ‘Refine?’ box indicates your choice to refine the result of the
sum. A Delete button can be used to remove it. This window shows the restraints to be used in a refinement.
It is organized into several tabbed pages, one page for each type of restraint.
Restraints are developed for an individual phase and act as additional
observations to be “fitted” during the refinement. 1. Select the tab for the
restraint type you wish to use. Each will have the same possibilities in the ‘Edit’ menu. 2. You can change the Restraint weight factor – this is used
to scale the weights for the entire set of restraints of this type. Default
value for the weight factor is 1.0. 3. You can choose to use or not
use the restraints in subsequent refinements. Default is to use the restraints. 4. You can change the search
range used to find the bonds/angles that meet your criteria for restraint. 5. You can examine the table of
restraints and change individual values; grayed out regions cannot be changed.
The ‘calc’ values are determined from the atom
positions in your structure, ‘obs’ values are the
target values for the restraint and ‘esd’ is the
uncertainty used to weight the restraint in the refinement (multiplied by the
weight factor). 6. Menu ‘Edit’ – some entries may be grayed out if not appropriate for your
phase or for the selected restraint. a. Select
phase –
active if there is more than one phase in your project. A dialog box will
appear with a list of the phases, select the one you want for restraint
development. b. Add
restraints –
this takes you through a sequence of dialog boxes which ask for the identities
of the atoms involved in the restraint and the value to be assigned to the
restraint. The esd is given a default value which can
be changed after the restraints are created. c. Add
residue restraints
– if the phase is a ‘macromolecule’ then develop the restraints from a selected
‘macro’ file based on those used in GSAS for this purpose. A file dialog box is
shown directed to /GSASIImacros; be sure to select
the correct file. d. Plot
residue restraints
– if the phase is a ‘macromolecule’ and the restraint type is either ‘Torsion restraints’ or ‘Ramachandran restraints’, then a plot
will be made of the restraint distribution; torsions as 1-D plots of angle vs.
pseudopotential energy and Ramachandran ones as 2-D plot of psi vs phi. In each
case a dialog box will appear asking for the residue types or specific torsion
angles to plot. Each plot will show the observed distribution (blue) obtained
from a wide variety of high resolution protein structures and those found (red
dots) for your structure. The restraints are based on a pseudopotential (red
curve or contours – favorable values at the peaks) which has been developed
from the observed distributions for each residue type. e. Change
value – this
changes the ‘obsd’ value for selected restraints; a
dialog box will appear asking for the new value. f.
Change esd – this changes the ‘esd’ value for selected restraints; a dialog box will
appear asking for the new value. g. Delete
restraints –
this deletes selected restraints from the list. A single click in the blank box
in the upper left corner of the table will select/deselect all restraints. This window shows the rigid body
models that have been entered into GSAS-II for this project. There are two
tabs; one is for vector style rigid bodies and the other is for flexible
“Residue” rigid bodies. Note that these rigid bodies must be inserted into one
of the phases before it can take effect in the crystal structure description. 1. Select the tab for the rigid
body type you wish to use. Each will have the different possibilities in the ‘Edit’ menu depending on whether a rigid
body has been defined. 2. Menu ‘Edit’ – the entries listed below depend on which type of rigid body
is selected. a.
Add rigid body – (Vector rigid bodies) this
creates a vector description of a rigid body. A dialog box asks the number of
atoms (>2) and the number of vectors required to create the rigid body. An
entry will be created showing a magnitude with the vector set to be applied for
each vector needed to develop the rigid body. b. Import
XYZ –
(Residue rigid bodies) this reads a text file containing a set of Cartesian
coordinates describing a rigid body model. Each line has atom type (e.g. C, Na,
etc.) and Cartesian X, Y and Z. c. Define
sequence –
(Residue rigid bodies) this defines a variable torsion angle in a sequence of
dialog boxes. The first one asks for the origin and the second asks for the pivot
atom for the torsion from the nearest neighbors to the origin atom; the atoms
that ride on the selected torsion are automatically found from their bond
lengths. d. Import
residues –
(Residue rigid bodies) this reads a predetermined macro file that contains
standard (Engh & Huber) coordinates for the amino
acids found in natural proteins along with predetermined variable torsion angle
definitions. 3. Once a rigid body is defined
you can plot it, change its name or manipulate any torsion angle to see the
effect on the plot. 4. The translation magnitudes in
a vector rigid body can be refined. This tree entry is
available after a sequential refinement has been run. (See the Controls tree item to set the histograms to be
used in a sequential refinement and use the Calculate/Sequential
refine menu command to run the refinement.)
When this is selected, the window tabulates the
sequential refinement results. The columns are the parameter names; the
naming convention is ‘p:h:name:n’ where ‘p’ is the phase number,’ h’ is the
histogram number, ‘name’ is the parameter name, and ‘n’ (if needed) is the item
number (e.g. atom number). The rows are the data sets used in the sequential
refinement. These are shown in the data tree
with a prefix of ‘PWDR’, ’HKLF’, ‘IMG’, or ‘PDF’ and usually a file name. These
constitute the data sets (‘Histograms’) to be used by GSAS-II for analysis.
Selection of these items does not produce any information in the data window
but does display the data in the Plots Window. They are described below. 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; the difference curve can be moved to another
position by clicking on it and then dragging it to a new
position. Reflection positions are shown with small vertical
lines. These can also be repositioned by dragging them. 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.
Menu Commands
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).
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 which is displayed.
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 with more than one powder pattern:
1. GSAS-II Data Tree
What
can I do here?
2. GSAS-II Data Editing Window
3. GSAS-II Plots Window
4. Main GSAS-II menu commands
Note that nonstandard space group symbols are permitted;
space group names must have spaces between the axial fields
(e.g. use ‘P n a 21’ not ‘Pna21’).
5. GSAS-II data tree items
Notebook
What can I do here?
Controls
What can I do here?
Covariance
What is plotted here?
What can I do with the plot?
Constraints
What can I do here?
Restraints
What can I do here?
Rigid bodies
What can I do here?
Sequential refinement results
What
can I do here?
1. Select a row – this will display the variance-covariance
matrix for the refinement with that data set.
2. Select a
column – this will display a plot of
that parameter across the sequence of data sets. Error bars for each value are
also shown.
3. Menu ‘File’ –
a. Save – this will create a text file of selected
columns with values and corresponding esds. A file
dialog box will appear; give a suitable file name; you may change directory if
desired.
6. Histogram data tree items
6A. Powder Histograms -
type PWDR
What can I do here?
What is plotted here?
What can I do with the plot?
For line plots:
For line plots in waterfall mode (multiple patterns are shown) these key press items are defined:
- 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: offset down
- for a waterfall plot of multiple powder profiles, increase the offset down.
- u: offset up
- for a waterfall plot of multiple powder profiles, increase the offset up.
- 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.
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.
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.
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’,
‘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.
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 = 2p/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 ‘File’ –
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.
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 show the various sample dependent parameters for this 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?
1. Menu ‘File’ –
a. Load – this loads
sample parameters from a previously saved .samprm
file.
b. Save – this saves
the sample parameters to a file with the extension ’.samprm’. A file dialog box
will appear to ask for the file name.
c.
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.
d.
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.
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:
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.
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 window shows the controls and results from indexing of
the peaks in the Index_Peak_List.
What can I do here?
1.
Select Bravais
Lattices – the selected are tried for
indexing the powder pattern.
2. 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.
3. Start
Volume – this sets an initial unit
cell volume for the indexing. It rarely needs to be changed.
4. Menu ‘Cell Index/Refine’ –
a. Index
Cell – this starts the indexing
process. 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.
b. Copy
Cell – this copies selected
solution to the Unit cell values; attention is paid to the Bravais lattice
shown for the choice and you may select a Space
group from the pull down box. Press Show
hkl positions to give the allowed peaks; to confirm the indexing compare
these to peak positions and any unfitted peaks in the pattern.
c. Refine
cell – this refines the copied
lattice parameters and optionally the Zero
offset. The results will be placed in the Indexing Result table with ‘use’
selected.
d. Make
new phase – this 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.
5. Select
another solution – the plot will show (red
dashed lines) the generated
reflection positions for the choice; compare them to the peak positions (blue
lines) and any unfitted peaks for conformation.
6. Select ‘keep’ – this preserves this solution for a subsequent indexing run; otherwise all solutions are erased before the indexing trial begins.
Reflection Lists
This window shows the reflections for the selected phase found in this powder data set. It is generated by a Rietveld or Pawley refinement.
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.
6B. Single Crystal Histograms – type HKLF
Instrument Parameters
This window shows the histogram type (SXC or SNC) and the wavelength. You may change the wavelength but rarely will need to do so.
HKL Plot Controls
This controls the display of the single crystal reflections on the plot. If available a green ring is shown for F-observed, a blue ring for F-calculated and a central disk for ΔF (green for Fo>Fc and red for Fo<Fc).
What
can I do here?
1. Change
the scale –
move the slider, the rings will change their radius accordingly.
2. Select
the zone – select
between 100, 010 or 001; plot axes will be labeled accordingly.
3. Select
plot type –
the choices are either F or F2, ΔF2/σ(F2), ΔF2>σ(F2) or ΔF2>3σ(F2).
4. Select
layer – move
the slider for upper layers for the selected zone.
Reflection
List
This window shows the reflections for this single crystal
data set.
6C. Pair Distribution Functions - type PDF
A PDF entry is created from a powder histogram (PWDR entry) using the Setup PDFs entry in the Calculate menu. The main PDF data tree item displays the same window as the PDF Controls, below. When this item is selected, the S(Q) function is plotted, see below.
PDF Controls
This window provides parameters for computing the pair distribution function [PDF, G(r)] from the I(Q) function. This can only be done when a chemical formula and appropriate control values are provided. If so, clicking on this menu item causes the I(Q), S(Q), F(Q) and G(R) functions to be plotted, as described below.
The Optimize PDF button can be used to refine the values of the "Flat Bkg", "Background ratio" and "Ruland width" parameters to best agree with the -4*pi*r line that is plotted for r < Rmin. Rmin should be set to a distance below the shortest expected interatomic distance for the material.
What can I do here?
The PDF parameters can be changed, triggering recomputation of the I(Q), S(Q), F(Q) and G(R) functions. Available menu commands are:
- Add element
- Adds a new element to the chemical formula by clicking on a periodic table. Note that the number of atoms of this type in the empirical formula must still be entered.
- Delete element
- Removes a previously-entered element from the chemical formula.
- Copy Controls
- Copies the current PDF control values to other PDF data entries
- Load Controls
- Replaces the current PDF control values with values read from a file (see Save controls).
- Save Controls
- Saves the current PDF control values into a file.
- Compute PDF
- Recomputes the PDF for the current entry. This is usually done automatically when values are changed, but if not this can be forced with this menu item.
- Compute all PDFs
- Recomputes the PDFs for all selected PDF entries. This is usually done after Copy Controls is used. By default PDFs are optimized to reduce the low G(r) region, but this can be turned off.
What is plotted here?
When a chemical formula and appropriate control values are provided, clicking on this menu item causes the I(Q), S(Q), F(Q) and G(R) functions to be plotted, as described separately, below.
What can I do with the plot?
For each of the plots, the following keyboard shortcuts are available:
For line plots with more than one powder pattern:
- c: contour on/off
- if multiple PDFs are available, then a contour plot is shown for the displayed function. All data sets must be the same length as the first one to be included in the contour plot.
- m: toggle multiple plot
- for multiple PDFs, this will show only the one selected from the data tree. The offset options are not active. Or all selected items will be plotted on a single axis.
- s: toggle single plot
- for multiple PDFs, this will show only the one selected from the data tree. The offset options are not active. Or all selected items will be plotted on a single axis.
- f: select data
- Allows only some PDFs to be plotted, rather than all.
- t: toggle legend
- provides a legend with the line type and name for each PDF.
For line plots in waterfall mode (multiple patterns are shown) these key press items are defined:
- t: toggle legend
- provides a legend with the line type and name for each PDF.
- 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: offset down
- for a waterfall plot of multiple powder profiles, increase the offset down.
- u: offset up
- for a waterfall plot of multiple powder profiles, increase the offset up.
- o: reset offset
- for a waterfall plot of multiple powder profiles, reset to no offset.
I(Q) Function
This shows the I(Q) function. See the PDF Controls for information on menu commands and plot options,
S(Q) Function
This shows the S(Q) function. See the PDF Controls for information on menu commands and plot options,
F(Q) Function
This shows the F(Q) function. See the PDF Controls for information on menu commands and plot options,
G(r) Function
This shows the PDF, G(r) function. See the PDF Controls for information on menu commands and plot options,
6D. 2-D Images – type IMG
Comments
This window shows whatever comment lines found in a “metadata” file when the image 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.
Image Controls
This window displays calibration values needed to
convert pixel locations to two-theta and azimuth. Also shown are
controls that determine how integration is performed.
Menu command for this window are used to perform calibration (fitting
the calibration values from a diffraction pattern image taken with a
calibrant) and for integration. Other menu commands allow the values
on the window to be saved to a file, read from a file or copied to
other images. The "Xfer Angles" menu command scales the current
integration range for other images located at different detector
distances.
Masks
Image masks are used designate areas of an image that should not be
included in the integration, typically used due to detector
irregularities, shadows of the beamstop, single-crystal peaks from a
mounting, etc. Masks can be created with a menu command or with
keyboard/mouse shortcuts.
There are five types of masks:
Masks of each type are created using the appropriate menu commands and
then clicking as described in the section on "What can I do with the
plot?" below, or by using keyboard shortcuts, also described in that
section.
The image is shown, as described above. Note that
The frame mask, if defined, is displayed in green, while
the other types of masks are shown in red.
There are menu commands to create masks as well as keyboard
shortcuts. If a menu command is used, then use left and right mouse
clicks as described below.
Create Spot masks after a menu command by clicking on
the location on the image that should be masked. There are also
two ways to create spot masks with the keyboard:
The default size for newly-created spot
masks is determined by the Spot_mask_diameter
configuration variable or 1.0 mm, if not specified.
Edit Spot mask location by left-clicking inside
or on the edge the of the mask and then drag the spot mask to a new
location.
Edit Spot mask radius by
right-clicking* inside
the mask and then dragging to change the mask size.
Create Ring masks with a menu command and then by left-clicking on
the mask center; Or, by pressing the
'r' key and then left-clicking.
(Right-click* to cancel.)
The default thickness for newly-created ring
masks is determined by the Ring_mask_thickness
configuration variable or 0.1 degrees
(2theta) if not specified.
Edit Ring mask location by
left-clicking on either the inner or outer circle and drag the
circle to the new radius.
Edit Ring mask thickness by
right-clicking* either on the inner or outer circle and drag the
the circle change spacing between the inner and outer circle.
Create Arc masks with a menu command and then by left-clicking on
at the mask center; Or, by pressing the
'a' key and then left-clicking.
(Right-click* to cancel.)
The default size for newly-created ring
masks is determined by
configuration variables Edit Arc mask location by
left-clicking on either the inner or outer circle and drag the
circle to the new radius. Alternately, left-click on the upper or
lower arc limit (the straight lines) and drag them to rotate the
center of the arc azimuthal range to a new position.
Edit Arc mask thickness or range by
right-clicking* either on the inner or outer circle and drag the
the circle change spacing between the inner and outer
circle. Alternately, right-click* on the upper or
lower arc limit (the straight lines) and drag them to change the
arc azimuthal range.
Create Polygon masks with a menu
command and then by left-clicking successively on the vertices of the
polygon shape surrounding pixels to be excluded. After the last
point is defined, right-click*
anywhere to close the mask. Alternately, press the 'p' key and then
left-click, as before, to define the mask and right-click* anywhere to close the mask.
Edit Polygon mask by
left-clicking on any point at a vertex in the polygon mask and drag
that point to a new position. If the vertex is dragged to the same
position as any other vertex in the mask the dragged point is deleted.
Add a point to Polygon mask by
right-clicking* on any vertex and dragging. A new
point is added to the mask immediately after the selected point at
the position where the mouse is released.
Create a Frame mask with a menu
command and then by left-clicking successively on the vertices of a
polygon. After the last point is defined, right-click*
anywhere to close the frame mask. Alternately, press the 'f' key and then
left-click, as before, to define the mask and right-click* anywhere to close the mask.
Note that if a Frame mask already exists, using the 'f' key or the
"Create Frame" menu item causes the existing frame mask to be deleted.
Edit the Frame mask by
left-clicking on any point at a vertex in the frame mask and drag
that point to a new position. If the vertex is dragged to the same
position as any other vertex in the mask the dragged point is deleted.
Add a point to the Frame mask by
right-clicking* on any vertex and dragging. A new
point is added to the mask immediately after the selected point at
the position where the mouse is released.
* Note that on a Mac with a
one-button mouse, a right-click is generated by pressing the control
button while clicking the mouse.
...
...
...
When a phase is selected from the data tree,
parameters are shown for that selected phase in a tabbed window. Clicking on
each tab raises the windows listed below. Each tab is identified by the
underlined phrase in the following: This gives overall parameters describing the phase such as
the name, space group, the unit cell parameters and overall parameters for the
atom present in the phase. It also has the controls for computing Fourier maps
for this phase. 1.
Menu ‘Compute’ –
The compute menu shows computations that are possible for this phase. a.
Fourier maps – compute Fourier maps
according to the controls set at bottom of General page. b.
Search maps – search the computed Fourier
map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
procedure; they will be printed on the console and will be shown in the ‘Map peaks’ page. This page will immediately be
shown and the peaks will be shown on the structure drawing for this phase as
white 3-D crosses. c.
Charge flipping – This performs a charge
flipping ab initio structure solution
using the method of Oszlanyi & Suto (Acta Cryst. A60, 134-141, 2004). You
will need to select a source for the reflection set and perhaps select an
element for normalization by its form factor, a resolution limit (usually 0.5A)
and a charge flip threshold (usually 0.1); these are found at the bottom of the
General window. A progress bar
showing the charge flip residual is shown while the charge flip is in
operation. When the residual is no longer decreasing (be patient – it doesn’t
necessarily fall continuously), press the Cancel
button to stop the charge flipping. The resulting map will be positioned to
properly place symmetry operators (NB: depends on the quality of the resulting
phases), searched for peaks and the display shifts to Map peaks to show them. d.
Clear map – This clears any
Fourier/charge flip map from memory; the Fourier map controls are also cleared. 2.
The items in the upper part of the General page that can be
changed are Phase name, Phase type, Space group, unit cell parameters &
refine flag. These are described in turn: a.
Phase name – this is the name assigned
to this phase. It should only be changed when the phase is initialized or
imported. b.
Phase type – this can only be set when
there are no atoms in the Atoms page for this phase. Select it when the phase
is initialized. c.
Space group – this should be set when
the phase is initialized; it can be changed later. Be careful about the impact
on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any
legal space group symbol using the short Hermann-Mauguin forms; put a space
between the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’). For space groups with a
choice of origin (e.g. F d 3 m), GSAS-II always uses the 2nd setting
where the center of inversion is located at the origin. The choice of space
group will set the available unit cell parameters. d. Refine
unit cell –
set this flag to refine the unit cell parameters in a Rietveld or Pawley
refinement. The actual parameters refined are the symmetry allowed terms (A0-A5)
in the expression e.
a, b, c, alpha, beta, gamma – lattice parameters; only
those permitted by the space group are shown. The volume is computed from the values entered. 3.
If there are entries in the Atoms page then the Elements
table is shown next on the General page; you may select the isotope (only
relevant for neutron diffraction experiments). The density (just above the
Elements) is computed depending on this choice, the unit cell volume and the
atom fractions/site multiplicities in the entries on the Atoms page. 4.
Next are the Pawley controls. a.
Do Pawley refinement? – This must be chosen to
perform a Pawley refinement as opposed to a Rietveld refinement for this phase.
NB: you probably should clear the Histogram scale factor refinement flag
(found in Sample parameters for the
powder data set) as it cannot be refined simultaneously with the Pawley
reflection intensities. b.
Pawley dmin – This is the minimum
d-spacing to be used in a Pawley refinement. NB: be sure to set this to match the minimum d-spacing indicated by
the powder pattern limits (see Limits
for the powder data set). c.
Pawley neg. wt. – This is the weight for a
penalty function applied during a Pawley refinement on resulting negative
intensities. Use with caution; initially try very small values (e.g. .01). A
value of zero means no penalty is applied. 5.
Fourier map controls are shown next on the General page. A
completed Rietveld or Pawley refinement is required before a Fourier map can be
computed. Select the desired type of map, the source of the reflection set and
the map resolution desired. The peak cutoff is defined as a percentage of the
maximum and defines the lowest level considered in the peak search. 6.
Charge flip controls are below the Fourier map controls. a.
Reflection set from – This is the source of structure
factors to be used in a charge flip calculation. These may be either a single
crystal data set, or structure factors extracted from a powder pattern via a
Pawley refinement or a Rietveld refinement. b.
Normalizing element – This is an element form factor
chosen to normalize the structure factors before charge flipping. None (the default) can be selected from
the lower right of the Periodic Table display shown when this is selected. c.
Resolution – This is the resolution of
the charge flip map; default is 0.5A. The set of reflections is expanded to a
full sphere and zero filled to this resolution limit; this suite of reflections
is then used for charge flipping. d. k-Factor – This is the threshold on
the density map, all densities below this are charge flipped. e. k-Max – This is an upper threshold
on the density may; all densities above this are charge flipped. In this way
the “uranium solution” problem is avoided. Use k-Max = 10-12 for equal atom
problems and larger for heavy atom ones. 7. Monte Carlo/Simulated Annealing
controls are at the bottom of the window. (Future capability & under
development). a. Reflection
set from –
This is the source of structure factors to be used in a charge flip
calculation. These may be either a single crystal data set, or structure factors
extracted from a powder pattern via a Pawley refinement or a Rietveld
refinement. b.
d-min - This restricts the set of
reflections to be used in the MC/SA run. c.
MC/SA algorithm – This selects the
type of jump to be used for each MC/SA trial. d.
Annealing schedule – This selects the
beginning MC/SA “temperature”, final “temperature”, slope and number of trials
at each step. e.
A-jump & B-jump – If the “Tremayne”
algorithm is chosen these determine the jump components for each trial.
This tab serves several
purposes. It is used to link histograms to the selected phase and it
allows the values and refinement flags to be set for the parameters
that are defined for each histogram-phase pair, labeled as HAP
parameters.
[Note that some GSAS-II parameters are defined for each phase (atomic positions, for example),
other parameters are defined for each histogram (scale factors and
instrumental constants, for example) but the HAP parameters have
values for each histogram in each phase.] It can also be used to show
a graphical representation of an HAP parameter set.
The HAP parameters include: the phase fraction; the sample contribution to peak broadening:
microstrain and crystallite size; a LeBail intensity extraction flag;
hydrostatic/elastic strain shifts to
lattice parameters; corrections to peak intensities due to
experimental effects (preferred orientation, extinction and disordered
solvents). This is the table of parameters for
the atoms in this crystal structure model. The menu controls allow manipulation
of the values, refinement flags as well as initiate calculations of geometrical
values (distances & angles) among the atoms. 1.
Atom
selection from table
- These are controlled by the mouse and the Shift/Ctrl/Alt keys: a.
Left Mouse Button (LMB) – on a row number selects
the atom. b.
Shift LMB – on a row number selects
all atoms from last selection to the selected row (or top is none previously
selected). c.
Ctrl LMB – on a row number
selects/deselects the atom. d.
Alt LMB – on a row number selects
that atom for moving; the status line at bottom of window will show name of
atom selected. Use Alt LMB again to
select a target row for this atom; insertion will be before this row and the
table will be updated to show the change. NB: the Draw Atoms list is not updated by this change. 2.
Double
left click a Type column heading: a dialog box is shown that allows you to select
all atoms with that type. 3.
Double
click a refine or I/A column heading: a dialog box will be shown with choices to be applied to
every atom in the list. 4.
Atom data item editing tools – These are controlled by
the mouse (Alt ignored, Shift & Ctrl allow selection of multiple cells but no use is made of them).
An individual data item can be cut/pasted anywhere including from/to another
document. Bad entries are rejected. If any entry is changed, press Enter key or select another atom entry
to apply the change. a.
Name – can change to any text
string. b.
Type – causes a popup display of
the Periodic Table of the elements; select the element/valence desired; the
atom will be renamed as well. c.
refine – shows a pulldown of
allowed refinement flag choices to be shown; select one (top entry is blank for
no refinement). d.
x,y,z – change atom coordinate.
Fractions (e.g. 1/3, 1/4) are allowed. e.
frac,Uiso,Uij – change these values;
numeric entry only. f.
I/A – select one of I(sotropic)
or A(nisotropic);
the Uiso/Uij entries
will change appropriately. 5.
Menu ‘Edit’
- The edit menu shows operations that can be performed on your selected
atoms. You must select one or more atoms before using many of the menu items. a. Append atom – add an H atom (name= Unk)
at 0,0,0 to the end of the atom table, it is also drawn as an H atom in the
structure plot. b. Append view point – add an H atom
(name= Unk) to the end of the atom table with coordinates matching the location
of the view point, it is drawn as an H atom in the structure plot c. Insert atom – insert an H atom (name=
Unk) at 0,0,0 before the selected atom, it is also drawn as an H atom in the
structure plot. d. Insert view point – insert an H atom
(name= Unk) before the selected atom with coordinates matching the location of the
view point, it is also drawn as an H atom in the structure plot. e. Delete atom – selected atoms will be
deleted from the atom list, they should also vanish
from the structure drawing. f.
Set atom
refinement flags – A popup dialog box appears; select refinement flags to
apply to all selected atoms. g. Modify atom parameters – A popup dialog
box appears with a list of atom parameter names; select one to apply to all
atoms. Name will rename selected
atoms according to position in table (e.g. Na(1) for Na atom as 1st
atom in list in row ‘0’). Type will
give periodic table popup; selected element valence will be used for all
selected atoms and atoms names will be changed. I/A will give popup with choices to be used for all selected atoms.
x,y,z will give popup for shift to
be applied to the parameter for all selected atoms. Uiso and frac will give popup for new
value to be used for all selected atoms. h. Transform atoms – A popup dialog box
appears; select space group operator/unit cell translation to apply to the
selected atoms. You can optionally force the result to be within the unit cell
and optionally generate a new set of atom positions. i.
Reload
draw atoms – 6. Menu ‘Compute’ – a. Distances & Angles – compute
distances and angles with esds (if possible) for selected atoms. A popup dialog
box will appear with distance angle controls. NB: if atoms have been added or
their type changed, you may need to do a Reset
of this dialog box before proceeding.
A plot that shows the atoms of the crystal structure is generated. The
atoms are displayed
according to the controls in the in this page as well as options on
the Draw Atoms page.
...
This gives a list of the atoms and
bonds that are to be rendered as lines, van der Waals radii balls, sticks,
balls & sticks, ellipsoids & sticks or polyhedra. There are two menus
for this tab; Edit allows modification of the list of atoms to be rendered and
Compute gives some options for geometric characterization of selected atoms. 1. Atom Selection from table: select
individual atoms by a left click of the mouse when pointed at the left most
column (atom numbers) of the atom display; hold down the Ctrl key to add to
your selection; a previously selected atom will be deselected; hold down Shift
key to select from last in list selected to current selection. A selected atom
will be highlighted (in grey) and the atoms will be shown in green on the plot.
Selection without the Ctrl key will clear previous selections. A double left
click in the (empty) upper left box will select or deselect all atoms. 2. Atom Selection from plot: select an
atom by a left click of the mouse while holding down the Shift key and pointed
at the center of the displayed atom, it will turn green if successful and the
corresponding entry in the table will be highlighted (in grey); any previous
selections will be cleared. To add to .your selection use the right mouse
button (Shift down); if a previously selection is reselected it is removed from
the selection list. NB: beware of
atoms that are hiding behind the one you are trying to select, they may be
selected inadvertently. You can rotate the structure anytime during the selection
process. 3. Double left click a Name, Type and Sym Op
column heading: a dialog box is shown that allows you to select all atoms
with that characteristic. For example, selecting the Type column will show all
the atom types; your choice will then cause all those atoms to be selected. 4. Double left click a Style, Label or Color
column: a dialog box is shown that allows you to select a rendering option
for all the atoms. For Color a color choice dialog is displayed that covers the
entire color spectrum. Choose a color by any of the means available, press the
“Add to Custom Colors”, select that color in the Custom colors display and then
press OK. NB: selecting Color will
make all atoms have the same color and for Style “blank” means the atoms aren’t
rendered and thus the plot will not show any atoms or bonds! 5. Menu
‘Edit’ - The edit menu shows
operations that can be performed on your selected atoms. You must select one or
more atoms before using any of the menu items. a. Atom style – select the rendering style
for the selected atoms b. Atom label – select the item to be
shown as a label for each atom in selection. The choices are: none, type, name
or number. c. Atom color – select the color for the
atom; a color choice dialog is displayed that covers the entire color spectrum.
Choose a color by any of the means available, press the “Add to Custom Colors”,
select that color in the Custom colors display and then press OK. d. Reset atom colors – return the atom
color back to their defaults for the selected atoms. e. View point – position the plot view
point to the first atom in the selection. f.
Add atoms
– using the selected atoms, new ones are added to the bottom of the list after
applying your choice of symmetry operator and unit cell translation selected
via a dialog display. Duplicate atom positions are not retained. Any
anisotropic thermal displacement parameters (Uij) will be transformed as
appropriate. g. Transform atoms – apply a symmetry
operator and unit cell translation to the set of selected atoms; they will be
changed in place. Any anisotropic thermal displacement parameters (Uij) will be
transformed as appropriate. h. Fill CN-sphere – using the atoms
currently in the draw atom table, find all atoms that belong in the
coordination sphere around the selected atoms via unit cell translations. NB:
symmetry operations are not used in this search. i.
Fill unit
cell - using the atoms currently selected from the draw atom table, find
all atoms that fall inside or on the edge/surface/corners of the unit cell.
This operation is frequently performed before Fill CN-sphere. j.
Delete
atoms – clear the entire draw atom table; it is then refilled from the
Atoms table. You should do this operation after any changes in the Atoms table,
e.g. by a structure refinement. 6. Menu
‘Compute’ - The compute menu gives a
choice of geometric calculations to be performed with the selected atoms. You
must select the appropriate number of atoms for these to work and the
computation is done for the atoms in selection order. a. View pt. dist. - this calculates
distance from view point to all selected draw atoms; result is given on the
console window. b. Dist. Ang. Tors. – when 2-4 atoms are selected, a distance, angle or torsion
angle will be found for them. The angles are computed for the atoms in their
selection order. The torsion angle is a right hand angle about the A2-A3 vector
for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given
for the calculated value if a current variance-covariance matrix is available.
The result is shown on the console window; it may be cut & pasted to
another application (e.g. Microsoft Word). c. Best plane – when 4 or more atoms are
selected, a best plane is determined for them. The result is shown on the
console window; it may be cut & pasted to another application (e.g. Microsoft
Word). Shown are the atom coordinates transformed to Cartesian best plane
coordinates where the largest range is over the X-axis and the smallest is over
the Z-axis with the origin at the unweighted center of the selection. Root mean
square displacements along each axis for the best plane are also listed. The
Z-axis RMS value indicates the flatness of the proposed plane. NB: if you select (e.g. all) atoms then
Best plane will give Cartesian coordinates for these atoms with respect to a
coordinate system where the X-axis is along the longest axis of the atom
grouping and the Z-axis is along the shortest distance. The origin is at the
unweighted center of the selected atoms.
A plot that shows the atoms of the crystal structure is generated. The
atoms are displayed
according to the controls in the in this page as well as options on
the Draw Options page.
...
This gives the list of
included Rigid bodies in this phase This
gives the list (magnitude, x y & z) of all peaks found within the unit cell
from the last Fourier/charge flip map search sorted in order of decreasing peak
magnitude. The crystal structure plot shows each peak position as a white to
dark gray cross; the shade is determined from the magnitude for the peak
relative to the maximum peak magnitude. 1. Peak Selection from table: select
individual atoms by a left click of the mouse when pointed at the left most
column (atom numbers) of the atom display; hold down the Ctrl key to add to
your selection; a previously selected atom will be deselected; hold down Shift
key to select from last in list selected to current selection. A selected atom
will be highlighted (in grey) and the atoms will be shown in green on the plot.
Selection without the Ctrl key will clear previous selections. A left click in
the (empty) upper left box will select or deselect all atoms. 2.
Select the mag
column – the entries will be sorted with the largest at the top. 3.
Select the dzero column – the entries will be
sorted with the smallest (distance from origin) at the top. 4.
Menu ‘Map
peaks’ – a.
Move
peaks – this copies selected peaks to the Atoms
list and the Draw Atoms list. They will be appended to the end of each
list each with the name ‘UNK’ and the atom type as ‘H’. They will also be drawn
as small white spheres at their respective positions in the structure drawing.
You should next go to the Atoms page and change the atom type to whatever element
you desire; it will be renamed automatically. b.
View
point – this positions the view point (large 3D RGB cross) at the 1st
selected peak. c.
View pt.
dist. – this calculates distance
from view point to all selected map peaks. d.
Calc dist/ang – if 2 peaks are
selected, this calculates the distance between them. If 3 peaks are selected
this calculates the angle between them; NB: selection order matters. If
selection is not 2 or 3 peaks this is ignored. Output is on the console window. e.
Equivalent
peaks – this selects all peaks related to selection by space group
symmetry. f.
Unique
peaks – this selects only the unique peak positions amongst those selected. g.
Delete
peaks – this deletes selected peaks. The shading on the remaining peaks is
changed to reflect any change in the maximum after deletion. h.
Clear
peaks – this deletes all the peaks in the map peak list; they are also
removed from the crystal structure drawing plot. This
gives the list of reflections used in a Pawley refinement and can only be seen
if the phase type is ‘Pawley’ (see General). 1. Menu
‘Operations’ – a.
Pawley
create – this creates a new set of Pawley reflections, over writing any
preexisting Pawley set. They are generated with d-spacings larger than the
limit set as ‘Pawley dmin’ in the General tab for this phase. By default the refine flags are not set and the Fsq(hkl) = 100.0. b.
Pawley
estimate – this attempts an estimate of Fsq(hkl) from the peak heights of
the reflection as seen in the 1st powder pattern of those selected
in the Data tab. c.
Pawley
delete – this clears the set of Pawley reflections. 2.
You can change the refine flags either by
clicking on the box or by selecting one and then selecting the column (a single
click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
clear the flags. You should deselect those reflections that fall below the
lower limit or above the upper limit of the powder pattern otherwise you may have
a singular matrix error in your Pawley refinement. 3. You
can change the individual Fsq(hkl) values by selecting it, typing in the new
value and then pressing enter or selecting somewhere else in the table. GSAS-II provides a number of configuration settings that can
be changed via variables that can be set and saved. These are
controlled in the File/Preferences menu item (on Mac the Preferences
menu is found in the usual place on Macs, in the main application menu). These
settings are optionally saved from for subsequent runs in a file named
config.py. More information about this can be found in the
appropriate section of the Programmer's documentation.
The
routines and classes used within GSAS-II are documented in a set of web
pages and in a PDF
document. This documentation is created from the Python source code files
using Sphinx.
What can I do here?
What is plotted here?
What can I do with the plot?
thickness: Ring_mask_thickness (0.1 degrees 2theta if not specified) and
azimuthal range: Arc_mask_azimuth (10.0 degrees if not specified.)
Stress/Strain
What can I do here?
What is plotted here?
What can I do with the plot?
6E. Powder Peaks – type PKS
6F. Small Angle Scattering – type SASD
7. Phase data tree items
General Phase Parameters
What
can I do here?
Data
What
can I do here?
Atoms
What
can I do here?
Draw Options
What
can I do here?
What is plotted here?
What can I do with the plot?
Draw Atoms
What
can I do here?
What is plotted here?
What can I do with the plot?
RB Models
Texture
What can I do here?
Map peaks
What can I do
here?
Pawley
reflections
What can I do here?
Layers
What can I do here?
Wave Data
What can I do here?
MC/SA
What can I do here?
Pawley reflections
What can I do here?
Macintosh
notes:
GSAS-II can be run on Windows, Linux and Macintosh/OS X computers, but
the GUI follows the native style of Mac OS X.
On Windows and some versions of Linux, the menu bars appears on top of
the main window.
On the Mac, the menu appears at the
location that has been configured for menus (usually at the top of the
screen).
GSAS-II defines actions for both the left and right buttons on a two-button mouse,
If a two or three-button mouse is used with a Mac, these mouse buttons
will work as intended. If using
a Mac touchpad or single-button
mouse, clicking the touchpad or mouse button will generate a "left
button" click. Hold down the control-key to generate a "right button" click.
Configuration Variables:
Programmers documentation
Last modified: Tue Nov 20 21:31:35 CST 2018