Description: GSAS-II logoHelp 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.

Help Index

  1. Learning GSAS-II: tutorials
  2. Application windows
  3. Main menu commands
  4. Data Tree headings, graphics windows and menu commands
    1. Top-level Data Tree headings
    2. Phase Data Tree headings
    3. Image (IMG) Data Tree headings
    4. Powder histogram (PWDR) Data Tree headings
    5. Single Crystal histogram (HKLF) Data Tree headings
    6. Pair Distribution Functions (PDF) Data Tree headings
    7. Powder Peaks (PKS) Data Tree headings
    8. Small Angle Scattering (SASD) Data Tree headings
  5. Other: Macintosh notes, Configuration options and Programmers documentation

GSAS-II tutorials:

The best way to learn about GSAS-II is to work through tutorials, which shows how to use different sections of the program. A list appears below. These tutorials can be viewed as web pages using the links below, but to actually perform the tutorial exercises, the sample data needs to be downloaded, which can be done most easily using the Help/Download tutorial menu entry. When this menu entry is used from inside GSAS-II (unless browse on web -- data not loaded is selected), data files (and optionally the web pages for off-line use) are downloaded.

Getting started

Rietveld fitting

Structure solution

Calibration/Image Processing

Strain/Texture

Small-Angle scattering

Other



1. Main GSAS-II data tree items

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 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. They do not change and are described below as the main menu commands section.



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, as described below in the data tree sections.



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 with the controls

toolbar on plots

The first nine icons are named: Home, Back, Forward, Pan, Zoom, Save, Key Press and Help, respectively. The remainder move or rescale the plot.

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.
Key Press
Shows a menu of key press commands that can be used to interact with the plot. These actions can be initiated from the menu.
Help
accesses GSASII help on the specific plot type.
{less than}
Shifts the plot to the left, relative to the axes
{greater than}
Shifts the plot to the right, relative to the axes
{up arrow}
Shifts the plot up, relative to the axes
{down arrow}
Shifts the plot down, relative to the axes
{less than}+{greater than}
Zooms in on the plot (magnifies) along the horizontal (x) direction to show more details.
{greater than}+{less than}
Zooms out on the plot (demagnifies) along the horizontal (x) direction.
{up arrow}/{down arrow}
Zooms in on the plot (magnifies) along the vertical (y) direction to show more details.
{down arrow}/{up arrow}
Zooms out on the plot (demagnifies) along the vertical (y) direction.

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.



4. Main GSAS-II menu commands

  1. Menu File
    Open project…
    Open a previously saved GSAS-II project file ({project}.gpx). If you currently have a project file open, you are asked if it is OK to overwrite it; Cancel will cancel the read process.

    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 Save As... menu command (you may wish to use name.gpx to overwrite the current version or select a new name.) If you forget specify a project name, then name.bak3 will be considered the project name and backups will then be named name.bak3.bak0.gpx, etc.

    Save project
    Save the current project. If this is a new project that has not yet been saved, you will be prompted for a new name in a file dialog (you may optionally change the directory in that dialog). If the file exists, you will be asked if it OK to overwrite it. Once a file name has been used to read or save a project, the name is shown after ‘Loaded Data:’ in the first item in the data tree.
    Save Project as...
    Save the current project in a specified project file. You will be prompted for a new name in a file dialog (you may optionally change the directory in that dialog). If the file exists, you will be asked if it OK to overwrite it.
    New Project
    Discards any changes made to the current project since the last save and creates a new empty project.
    Preferences
    Provides access to GSAS-II configuration settings, as described in the Configuration Variables section.
    Quit
    Exit the GSAS-II program. Discards any changes made to the current project since the last save. You can also exit GSAS-II by pressing the red X in the upper right (Windows) or left (Mac).
  2. Menu Data
    Read Powder Pattern Peaks…
    Read in a list of powder pattern peak positions as either a d-spacing table or a set of 2theta positions; these can be used in GSAS-II powder pattern indexing.
    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.
    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.
    Add new 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 Phase/General tab is opened for this phase, where you should first select the phase type, the enter the space group symbol and then the lattice parameters.
    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’).
    Delete data
    This will remove a phase from the data tree. A dialog box will present the list of phases; pick one (or more) to delete.
    Rename data
    Rename a histogram entry. This should only be done before the histogram is used in any phases: e.g. only rename data immediately after reading.
    Delete data
    This will remove an item from the data tree. A dialog box with a list of choices for histograms is presented. Do not remove histograms that are used in phases.
  3. Menu Calculate
    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.
    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 0th atom in the 0th phase while shift names have a ‘d’ in then, e.g. ‘0::dAx:0’. Press the window exit button to exit this dialog box.
    Refine
    This performs the refinement (Pawley/Rietveld or single crystal) according to the controls set in the Controls data tree item.
    Sequential refine
    This starts a sequential refinement with the data sets selected in the Controls data tree item.
  4. Menu Import

    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.

    Image
    Read in 2-D powder diffraction images (multiple patterns can be selected). 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. 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
    Phase
    Creates a new phase by reading unit cell/symmetry/atom coordinate information. GSAS-II can read information from a number of different format files including:
    GSAS .EXP
    This reads one phase from a (old) 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 this command. After selecting a phase, a dialog box is shown with the proposed phase name. You can change it if desired.
    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.
    CIF file
    This reads one phase from a Crystallographic Information File ({name}.CIF (or .cif). The file name is found in a directory dialog; you can change directories as needed. 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 this command. After selecting a phase, a dialog box is shown with the proposed phase name. You can change it if desired.
    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. If the selected file has more than one phase, a dialog is shown with the choices; If you want more than one, redo this command. After selecting a phase, a dialog box is shown with the proposed phase name. You can change it if desired.
    guess format from file
    This attempts to read one phase from a file trying the formats as described above. On occasion, this command may not succeed in correctly determining a file format. If it fails, retry by selecting the correct format from the list.
    Powder Data
    Reads a powder diffraction data set in a variety of formats. Results are placed in the GSAS-II data tree as ‘PWDR file name'. Information needed for processing a powder diffraction data set, such as data type, calibration constants (such as wavelength) and default profile parameters are read from a separate file, either a (old) GSAS instrument parameter file (usually .prm, .ins or .inst extension) or a new GSAS-II .instparm file.

    Note that it is possible to apply corrections to the 2-theta, intensity or weight values by creating a adding 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.

    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 one .cif can be chosen. If you want more than one, redo this command.
    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.
    GSAS .fxye files
    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 choice(s).
    TOPAS .xye 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.
    guess format from file
    This attempts to read one data set from a file trying the formats as described above. On occasion, this command may not succeed in correctly determining a file format. If it fails, retry by selecting the correct format from the list.
    Structure Factor
    Reads single crystal input from a variety of file types. Results are placed in the GSAS-II data tree as ‘HKLF file name’
    F**2 HKL file
    This reads squared 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 the file contains structure factors (as F**2) as the file itself has no internal indication of this.
    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 the file contains structure factors (as F values) as the file itself has no internal indication of this.
    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.
    guess format from file
    This attempts to read one data set from a file trying the formats as described above. However, since it cannot be determined if SHELX format .hkl contaings F or F**2 values, do not use this command for those files. On occasion, this command may not succeed in correctly determining a file format. If it fails, retry by selecting the correct format from the list.
    Small Angle Data
    Reads small angle scattering data from files. At present these formats are not documented; See the importer routines (file .../GSASII/imports/G2sad_xye.py) for more details.
  5. Menu Export

    GSAS-II uses separate routines to write out files with information 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.

    Entire project as
    At present the only supported format for a project is a Full CIF file. This brings up a separate window where information such as ranges for bond distances and angles can be selected.
    Phase as
    Phases can be exported in a variety of formats including a simplified CIF file that contains only the unit cell, symmetry and coordinates.
    Powder data as
    Powder data can be exported in number of formats. Note that this menu can also be used to export reflection lists from Rietveld and Pawley fits.
    Single crystal data as
    Single crystal reflection lists can be exported as text files or as a simplified CIF file that contains only structure factors.
    Image data
    This exports selected images as a portable networks graphics format (PNG) file. Alternately, the image controls and masks can be written for selected images. If strain analysis has been performed on images, the results can also be exported here as a spreadsheet (.csv file).
    Maps as
    Fourier maps can be exported here.
    Export all Peak Lists...
    This allows peak lists from selected powder histograms to be written to 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.
    Export HKLs
    This allows single crystal reflection lists from selected histograms to be written to a file.
    Export PDF...
    This allows computed PDFs peak lists from selected histograms to be written as 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 file name comes from the PDF entry in the GSAS-II data tree.


5. GSAS-II data tree items

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.

What can I do here?

Use the notebook to keep track of information related to how you use GSAS-II.

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. A text window is displayed with statistical values and goodness of fit parameters.

What is plotted here?

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 with 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.

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. 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).

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.


6. Histogram data tree items

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.

6A. Powder Histograms - type PWDR

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

What can I do here?

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).

What is plotted here?

The powder patterns that are part of your project are shown on this page. They can be displayed as a stack of powder patterns, just a single pattern or as a contour image of the peak intensities. What can be done here will depend on which is displayed.

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

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:

b: subtract background
Subtracts the fitted background from the powder pattern. Pressing this again turns the mode off.
n: log(I) on/off
changes the y-axis to be the log10 of the intensity; difference curve is not shown for log(I) on.
q: toggle Q plot
changes the x-axis from 2Theta to Q. This will put multiple powder patterns taken at different wavelengths/types on the same x-axis scale.
t: toggle Q plot
changes the x-axis from 2Theta to d-space. This will put multiple powder patterns taken at different wavelengths/types on the same x-axis scale. May not be very useful with data over a wide range.
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.

For line plots with more than one powder pattern:

c: contour on/off
if multiple powder profiles, then a contour plot is shown of the observed intensities. All data sets must be the same length as the first one to be included in the contour plot.
m: toggle single/multiple plot
for multiple powder profiles, this will show only the one selected from the data tree. The offset options are not active.
f: select data
Allows only some powder patterns to be plotted, rather than all.
+: no selection
for multiple powder profiles, only the observed curve is shown.

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 to the left.
r: offset right
for a waterfall plot of multiple powder profiles, increase the offset to the left.
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 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 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 Make new PDFs entry in the Calculate menu. The main PDF data tree item has no parameters and provides no new menu items. When this item is selected, the I(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.

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 PDF entries. This is usually done after Copy Controls is used.

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. 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 to the left.
r: offset right
for a waterfall plot of multiple powder profiles, increase the offset to the left.
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:

  1. Spot masks: occlude a circle with a selected center and diameter in image coordinates (mm).
  2. Ring masks: occludes a specific Bragg reflection (a ring placed relative to the image center). The location and thickness of the ring are specified in degrees 2-theta.
  3. Arc masks: occludes a section of a Bragg reflection, similar to a ring mask, except that in addition to the location and thickness of the ring, the mask has a starting and ending azimuthal angle.
  4. Polygon masks: occludes an arbitary region created by line segments joining a series of points specified in image coordinates (mm). Pixels inside the polygon mask are not used for integration.
  5. The Frame mask: occludes an arbitary region created by line segments joining a series of points specified in image coordinates (mm). Typically a point is placed near each corner of the image. Only pixels inside the frame mask are used for integration. Only one frame mask can be defined.
What can I do here?

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.

What is plotted here?

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.

What can I do with the plot?

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.

  1. Spot masks:

    Create Spot masks after a menu command by clicking on the location on the image that should be masked. There are also three ways to create spot masks with the keyboard:

    • Press the 's' key and then left-click on the mask location. (Right-click* to cancel.)
    • Press the 'm' key and then left-click successively on multiple locations for spot masks. Press the 'm' key again or right-click* to stop adding spot masks.
    • Move the mouse to the position for a new spot mask and press the 't' key. (Note that this can be used while the plot is in Zoom or Pan mode.)

    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.

  2. Ring masks:

    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.

  3. Arc masks: occludes a section of a Bragg reflection, similar to a ring mask, except that in addition to the location and thickness of the ring, the mask has a starting and ending azimuthal angle.

    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
    thickness: Ring_mask_thickness (0.1 degrees 2theta if not specified) and
    azimuthal range: Arc_mask_azimuth (10.0 degrees if not specified.)

    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.

  4. Polygon masks: occludes an arbitary region created by line segments joining a series of points specified in image coordinates (mm). Pixels inside the polygon mask are not used for integration.

    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.

  5. The Frame mask: occludes an arbitary region created by line segments joining a series of points specified in image coordinates (mm). Typically a point is placed near each corner of the image. Only pixels inside the frame mask are used for integration. Only one frame mask can be defined.

    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.

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

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?
What is plotted here?

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.

What can I do with the plot?

...

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.

What is plotted here?

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.

What can I do with the plot?

...

RB Models

This gives the list of included Rigid bodies in this phase

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.

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 due to the different nature of the Mac, the program behaves slightly differently. On Windows and Linux, there are two menu bars: (A) found at the top of the GSAS-II data tree and (B) on GSAS-II data editing window. The latter changes, based on which data item is selected in the data tree. On the Mac, these menus are combined located on the location that has been configured for menus (usually at the top of the screen). The main manu and the data editing menu (if present) are separated by a vertical bar.

GSAS-II uses both the left and right buttons on a two-button mouse. If a mac has a two or three-button mouse attached, these mouse buttons will be used on the other platforms. If using a Mac touchpad or single-button mouse, the control-key should be held down to simulate use of the right mouse button. The left button click is generated otherwise.

Configuration Variables:

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, 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.

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.

 



Last modified: Tue Jan 3 12:18:13 CST 2017