Help
for GSAS-II
This
is where to find help on various GSAS-II windows and plots. Note that GSAS-II
operates with four windows: the main GSAS-II data tree
window, which provides a hierarchical view of the current project; the GSAS-II data editing window, which shows the contents of
a particular section of the project, where values can be examined and changed;
the GSAS-II Plots window, which shows graphical
representations of the results; and the console which has printout information
that can be selected, cut & pasted into a document.
Programmers 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.
GSAS-II tutorials:
Powder pattern peak picking, fitting and indexing
Lab X-ray powder pattern Rietveld refinement
CW Neutron powder pattern Rietveld refinement with
constraints
Combined neutron x-ray Rietveld
refinement and Fourier maps
Synchrotron X-ray powder pattern Rietveld refinement
Charge flipping
structure solution – jadarite & sucrose
Small angle X-ray data size distribution
Fitting Small Angle Scattering Data
1.
GSAS-II data tree
This
is a hierarchical view of the data items in your GSAS-II project (name.gpx).
Clicking on any item in the tree opens a window 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.
What can I do here?
The
menus associated with this window provide access to many features of GSAS-II,
as outlined below:
1. Menu ‘File’ –
a. Open project… - Open a previously saved GSAS-II project file (name.gpx). If you currently have a project file open, you are asked if it is OK to over write it; Cancel will cancel the process. NB: you may open a backup gpx file (e.g. name.bak3.gpx) to recover a previous version of your project. Remember to Save As… to e.g. name.gpx to overwrite the current version. Otherwise you will get backups of your backup file (e.g. name.bak3.bak0.gpx, etc.).
b. Save project – Save the current project. If a file name is shown after ‘Loaded Data:’ in the data tree, it will be saved there. Otherwise, you will be prompted for a new name in a file dialog (you may change directory as well). If the file exists, you will be asked if it OK to overwrite.
c. Save As… - Save the current project to a new file. A file dialog will be shown to enter the name (and change directory if desired). If the file exists, you will be asked if it OK to overwrite.
d. Close project – Close the current project; you will be asked if you want to save it first.
e. Exit – Exit the GSAS-II program; if there is a current project you will be asked if you want to save it first. Pressing the red X in the upper right (Windows) also exits (no save option) GSAS-II; useful for escaping from GSAS-II if needed.
2.
Menu
‘Data’ –
a. Read image data… - Read in 2-D powder diffraction images (multiple patterns can be selected). GSAS-II can read many different image file formats including MAR345 files, Quantum ADSC files, and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these formats have data fields that should contain relevant information for the exposure (e.g. wavelength), these are rarely filled in correctly by the data acquisition software. Thus, you should have separately noted this information as it will be needed
b. Read Powder Pattern Peaks… - Read in a list of powder pattern peak positions as either a d-spacing table or a set of 2Q positions; these can be used in GSAS-II powder pattern indexing.
c. Sum powder data – Form the sum of previously read powder patterns; each with a multiplier. Can be used to accumulate data, subtract background or empty container patterns, etc. Patterns used to form the sum must be of identical range and step size. Result is a new PWDR entry in the GSAS-II data tree.
d. Sum image data – Form the sum of previously read 2-D images; each with a multiplier. Can be used to accumulate data, subtract background or empty container patterns, etc. Images used to form the sum must be of identical size and source. Result is a new IMG entry in the GSAS-II data tree, and a GSAS-II image file is written for future use.
e. Add phase – This begins the creation of a new phase in the data tree (under Phases). You are first prompted in a dialog box for a name to be assigned to the new phase. Then the General tab is opened for this phase; you should first select the phase type, enter the space group symbol and then lattice parameters. Note that nonstandard space group symbols are permitted; there must be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).
f. Delete phase – This will remove a phase from the data tree. A dialog box will present the list of phases; pick one (or more) to delete.
g. Rename data – This might be a bad idea!! Don’t use this unless the data to be renamed has not been used anywhere in GSAS-II, e.g. only rename freshly read data.
h. Delete data – This will remove an item from the data tree. A dialog box with a list of choices is presented.
3. Menu ‘Calculate’ –
a. Make new PDFs – This creates the pair distribution function (PDF) controls for each powder pattern selected in the dialog box. See PDF Controls for further directions.
b. View LS parms – This shows a dialog box with all the parameters for your project; those to be refined are flagged ‘True’, otherwise ‘False’. Blanks indicate parameters that are not refinable. The total number of refined parameters is also shown at the top of the list. The value of each parameter is also given. The parameter names are of the form ‘p:h:name:id’ where ‘p’ is the phase index, ‘h’ is the histogram index and ‘id’ is the item index (if needed). Indexes all begin with ‘0’ (zero). Note that for atom positions the value is not a refinable parameter, but the shift in the value is. Position names are, e.g. ‘0::Ax:0’ for the x-position of the zeroth atom in the zeroth phase while shift names have a ‘d’ in then, e.g. ‘0::dAx:0’. Press the window exit button to exit this dialog box.
c. Refine – This performs the refinement (Pawley/Rietveld or single crystal) according to the controls set in the Controls data tree item.
d. Sequential refine – This starts a sequential refinement with the data sets selected in the Controls data tree item.
4. Menu ‘Import’ – A sub menu appears with choices for import of data. Each entry when selected with the mouse shows further submenus with specific imports that are available. Any of these files can be accessed from a zip file.
a. Phase -
1. from GSAS .EXP file - This reads one phase from a GSAS experiment file (name.EXP). The file name is found in a directory dialog; you can change directories as needed. Only .EXP (or .exp) file names are shown. If the selected file has more than one phase, a dialog is shown with the choices; only one can be chosen. If you want more than one, redo the Import/Phase/from GSAS .EXP file command. After selecting a phase, a dialog box is shown with the proposed phase name. You can change it if desired.
2. from PDB file - This reads the macromolecular phase information from a Protein Data Base file (name.PDB or name.ENT). The file name is found in a directory dialog; you can change directories as needed. Only .PDB (or .pdb) or .ENT (or .ent) file names are shown. Be careful that the space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions (e.g. with spaces between axial fields). A dialog box is shown with the proposed phase name. You can change it if desired.
3. from CIF file This reads one phase from a Crystallographic Information File (name.CIF). The file name is found in a directory dialog; you can change directories as needed. Only .CIF (or .cif) file names are shown. If the selected file has more than one phase, a dialog is shown with the choices; only one can be chosen. If you want more than one, redo the Import/Phase/from CIF file command. After selecting a phase, a dialog box is shown with the proposed phase name. You can change it if desired.
4. from GSAS-II gpx file This reads one phase from a GSAS-II project file (name.gpx). The file name is found in a directory dialog; you can change directories as needed. Only .gpx (or .GPX) file names are shown. If the selected file has more than one phase, a dialog is shown with the choices; only one can be chosen. If you want more than one, redo the Import/Phase/from GSAS-II gpx file command. After selecting a phase, a dialog box is shown with the proposed phase name. You can change it if desired.
5. guess format from file This attempts to read one phase from a file trying the formats as described above.
b.
Powder
Data – results are placed in the
GSAS-II data tree as ‘PWDR file
name’.
1.
from CIF file This
reads one powder pattern (histogram) from a Crystallographic Information File (name.CIF). The file name is found in a directory dialog;
you can change directories as needed. Only .CIF (or .cif)
file names are shown.; only one can be chosen. If you
want more than one, redo the Import/Powder
Data/from CIF file command.
2.
from GSAS-II gpx file This reads powder patterns from a previously
created GSAS-II gpx project file. If the selected
file has more than one powder pattern, a dialog is shown with the choices; one
or more can be selected. It will ask for an appropriate instrument parameter
file to go with the selected powder data sets.
3.
from GSAS file This
reads powder patterns (histograms) from the defined GSAS format powder data
files. GSAS file types STD, ESD, FXY and FXYE are recognized. Neutron TOF data
with a ‘TIME-MAP’ are also recognized. The file names are found in a directory
dialog; you can change directories as needed. If the selected files have more
than one powder pattern, a dialog is shown with the choices.
4.
from Topas xye file This reads
powder patterns (histograms) from the defined topas xye format powder data files. This format is a simple
3-column (2-theta, intensity & sig) text file. The file names are found in
a directory dialog; you can change directories as needed.
5. guess format from file This attempts to read one powder diffraction pattern (histogram) from a file trying the formats as described above.
c.
Structure
Factor – – results are placed in
the GSAS-II data tree as ‘HKLF file
name’.
1.
from F**2 HKL file This
reads structure factors (as F**2) and sig(F**2) from a SHELX format .hkl file. The file names are found in a directory dialog;
you can change directories as needed. You must know this is the content of this
file as it will have no internal indication of its contents.
2.
from F HKL file
This reads structure factors (as F) and sig(F) from a SHELX format .hkl file. The file names are found in a directory dialog;
you can change directories as needed. You must know this is the content of this
file as it will have no internal indication of its contents.
3.
from CIF file
This reads structure factors (as F**2 or F) and sig(F**2 or F) from a .CIF (or
.cif) or .FCF (or .fcf)
format file. The file names are found in a directory dialog; you can change
directories as needed. The internal structure of this file indicates in which
form the structure factors are used.
4.
guess format from
file This attempts to read one set of single crystal structure factors from
a file trying the formats as described above. One should not use this for SHELX
format files as the form of the structure factors is not indicated from within
the file.
5. Menu ‘Export’ –
a. Export Powder Patterns… - not yet implemented
b. Export All Peak Lists… - This writes the contents of the Peak List for all PWDR data onto a simple text file. There will be a heading for each PWDR GSAS-II tree item and columns of values for position, intensity, sigma and gamma follow.
c. Export HKLs… - not yet implemented
d. Export PDF… - This writes two simple text files name.gr and name.sq containing g(r) and s(q), respectively as 2 columns of data; a header on each indicated the source file name and the column headings. The name comes from the PDF entry in the GSAS-II data tree.
e. Export Phase… - not yet implemented
f. Export CIF… - not yet implemented
2.
GSAS-II Data Editing Window
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 described below.
Notebook
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.
Controls
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.
What can I do here?
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’.
Covariance
This
window contains final residual information; the GSASII Plots window ‘Covariance’ shows a graphical representation of the
variance-covariance matrix
Constraints
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. mstrain 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).
What can I do here?
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.
Restraints
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.
What
can I do here?
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.
Rigid
bodies
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.
What
can I do here?
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.
Sequential refinement results
In this window is tabulated the results of your sequential refinement. 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.
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.
Histograms
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.
Powder Histograms - PWDR
When
a powder diffraction data set (prefix ‘PWDR’) is selected from the data
tree, a
variety of subcategories in the tree are shown. The items that are shown depend
on the data set type. Selecting a subcategory raises the window listed below.
What can I do here?
1.
Menu
‘Analysis’ –
a. Analyze
– 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 < D/s < 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).
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. You can modify ‘changed’ as needed.
What can I do here?
1. You can change Tmin and Tmax in the ‘changed’
row as needed. Use the mouse to select the value to be changed (the background
on the box will be blue or have a black border or a vertical bar will appear in
the value), then enter the new value and press Enter or click the mouse
elsewhere in the Limits window. This will set the new value.
2. Modify the values of
‘changed’; this can be done on the plot by dragging the limit bars (left –
vertical green dashed line, right – vertical red dashed line) into position. A
left or right mouse click on a data point on the plot will set the associated
limit. In either case the appropriate value on the ‘changed’ row will be
updated immediately.
3. Menu ‘File’ –
a. 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.
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.
Sample Parameters
This
window show the various sample dependent parameters for this powder pattern.
The presence of a refine button indicates which can be refined while others are
fixed. All values can be changed in this window. 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
This
window shows the list of peaks that will be used by the peak fitting
refinement. It is filled by picking peaks in the powder pattern displayed in
the GSASII Plots window as a sequence of ‘+’ marks.
What
can I do here?
1.
Menu ‘Peak Fitting’ –
a. 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.
b. 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: there is only a
single level of recovery available.
c. LSQ PeakFit – perform 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 UnDo the refinement and reconsider your choice of
parameters to be varied.
d. 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.
e. Reset sig
and gam – this resets the values of sigma and gamma
to those computed from the instrument parameters U, V, W, X
& Y.
f. Clear peaks – this removes
all the peaks from the Peak List.
2.
You can add peaks to the Peak list using the mouse on the plot by: 1)
position the pointer near to the top point on a peak, 2) press the left mouse
button. The selected peak will be added to the Peak List in its correct sorted
order and a blue vertical line will be plotted on that position. Be sure that
the Zoom/Pan buttons are not selected on the Plot window. 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.
3.
You can move a Peak List item using the mouse on the plot by: 1) position
the pointer on the blue line for the peak you wish to move, 2) holding the left
mouse button down, drag to the desired position & then release the button.
The peak line will be drawn in the new position. Be sure that the Zoom/Pan
buttons are not selected on the Plot window.
4. 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.
5.
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; column should show in blue). Then type ‘y’ to set
the refine flags or ‘n’ to clear the flags.
6.
You can delete peaks in the Peak List by selecting rows (should appear in
blue) and then pressing the Delete key. You can also 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. Be sure
that the Zoom/Pan buttons are not selected on the Plot window.
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 List
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.
Single Crystal Histograms – 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.
Pair Distribution
Functions - PDF
PDF
Controls
This window
I(Q),
S(Q), F(Q) & G(R)
This
window...
2-D Images – 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...
Masks
This
window...
Phase Windows
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:
General Phase Parameters
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.
What can I do here?
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.
Data
sets
What can I do here?
Atoms
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.
What can I do here?
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 cup/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.
Draw Options
What can I do here?
Draw Atoms
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.
What can I do here?
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.
RB Models
This gives the list of included Rigid bodies
Texture
What can I do here?
Map peaks
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.
What can I do here?
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.
Pawley reflections
This gives the list of reflections used in a Pawley refinement and can only be seen if the phase type is ‘Pawley’ (see General).
What can I do here?
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.
3. GSAS-II Plots Window
This window presents all the graphical material as a
multipage tabbed set of plots utilizing the matplotlib python package. Each
page has a tool bar (at bottom in Windows) with the controls
These are Home, Back, Forward, Pan, Zoom, Save and Help,
respectively.
- Home: returns the plot to
the initial scaling
- Back: returns the plot to
the previous scaling
- Forward: reverses
the action in the previous press(es) of the Back button
- Pan: allows you to control
panning across the plot (press left mouse button) and zooming (press right
mouse button),
- Zoom: allows you to select a
portion of the plot (press right mouse button & drag for zoom box) for
the next plot.
- Save: allows you to save the
currently displayed plot in one of several graphical formats suitable for
printing or insertion in a document.
- Help: accesses GSASII help
on the specific plot type.
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.
The
specific types of plots that are pages in the GSASII Plots windows are next.
Powder Patterns
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 and on which item in the GSAS-II data
tree you have selected.
What can I do here?
1. Move the mouse cursor across
the plot, the plot status line will show the cursor position in 2Q, d-spacing and the
intensity. For a q-plot, q is shown instead of 2Q.
2. On the plot status line ‘key press’ – you can either press the key on the key board or select from the pull down menu. For line plots:
a. l: offset left – for a waterfall plot of multiple powder profiles, increase the offset to the left. Does not apply if only one pattern.
b. r: offset right - for a waterfall plot of multiple powder profiles, increase the offset to the left. Does not apply if only one pattern.
c. d: offset down - for a waterfall plot of multiple powder profiles, increase the offset down. Does not apply if only one pattern.
d. u: offset up - for a waterfall plot of multiple powder profiles, increase the offset up. Does not apply if only one pattern.
e. o: reset offset - for a waterfall plot of multiple powder profiles, reset to no offset. Does not apply if only one pattern.
f. 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.
g. 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.
h. q: toggle q plot – changes the x-axis from 2Q to q=2p/d. This will put multiple powder patterns taken at different energies on the same x-axis scale.
i. s: toggle single plot – for multiple powder profiles, this will show only the one selected from the data tree. The offset options are not active.
j. w: toggle divide by sig – for the pattern selected from the data tree, this will divide the observed, calculated and difference curves by the esd for the data points. Other data sets are not shown.
k. +: no selection - for multiple powder profiles, only the observed curve is shown.
3. For contour plots the status
line ‘key press’ options are different:
a. d:
lower contour max – this lowers the level
chosen for the highest contour color.
b. u:
raise contour max – this raises the level
chosen for the highest contour color
c. 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.
d. 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)!
e. c:
contour off/on – this turns off contouring
and returns to a waterfall plot with any offsets applied.
4. Depending on the item chosen
for the selected powder pattern in the data tree, the mouse buttons have
different actions:
a. Limits
- Modify the values of ‘changed’; this can be done on the plot by dragging the limit
bars (left – vertical green dashed line, right – vertical red dashed line) into
position. A left or right mouse click on a data point on the plot will set the
associated limit. In either case the appropriate value on the ‘changed’ row
will be updated immediately.
Covariance
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.
What can I do here?
1. 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.
2. Use the Zoom and Pan buttons to focus on some section of the variance-covariance matrix.
3. Type ‘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’.
Structure Factors
This plot shows...
What can I do here?
Powder Lines
This plot shows the line positions for the peak list
Powder Patterns
This plot shows….
What can I do here?
Peak Widths
This plot shows the contributions to the powder pattern peak
widths as Dd/d
(= Dq/q)
vs q(=2p/d)
from the Gaussian and Lorentzian parts of the profile function. The computed
curves are based on the values of U, V, W, X and Y shown in the Instrument
Parameters window in parentheses. These are the values for the instrument
contribution that were set when the powder pattern was first read in to
GSAS-II. If individual peak fitting has been performed, the values of ‘sig’
& ‘gam’ for the 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 individually
refined.
Texture
This plot shows...
What can I do here?
Sequential refinement
This plot shows the variation of the selected parameters
with respect to the data sequence number.
What can I do here?
2D Powder Image
This plot shows...
What can I do here?
2D Integration
This plot shows...
What can I do here?
2D Transformed Powder Image
This plot shows...
What can I do here?
Mustrain
This plot shows...
What can I do here?
Size
This plot shows...
What can I do here?
Preferred Orientation
This plot shows...
What can I do here?
Crystal Structure
This plot shows the atoms of the crystal structure. The atoms are displayed according to the controls in the Draw Options page.