4. GSAS-II Utility Modules¶
4.1. GSASIIpath: locations & updates¶
Routines for dealing with file locations, etc.
Determines the location of the compiled (.pyd or .so) libraries.
Interfaces with subversion (svn):
Determine the subversion release number by determining the highest version number
where SetVersionNumber()
is called (best done in every GSASII file).
Other routines will update GSASII from the subversion server if svn can be
found.
Accesses configuration options, as defined in config.py
-
GSASIIpath.
DoNothing
()[source]¶ A routine that does nothing. This is called in place of IPyBreak and pdbBreak except when the debug option is set True in config.py
-
GSASIIpath.
DownloadG2Binaries
(g2home, verbose=True)[source]¶ Download GSAS-II binaries from appropriate section of the GSAS-II svn repository based on the platform, numpy and Python version
-
GSASIIpath.
GetBinaryPrefix
(pyver=None)[source]¶ Creates the first part of the binary directory name such as linux_64_p3.9 (where the full name will be linux_64_p3.9_n1.21).
Note that any change made here is also needed in GetBinaryDir in fsource/SConstruct
-
GSASIIpath.
GetConfigValue
(key, default=None)[source]¶ Return the configuration file value for key or a default value if not present
Parameters: - key (str) – a value to be found in the configuration (config.py) file
- default – a value to be supplied if none is in the config file or the config file is not found. Defaults to None
Returns: the value found or the default.
-
GSASIIpath.
GetVersionNumber
()[source]¶ Return the maximum version number seen in
SetVersionNumber()
-
GSASIIpath.
IPyBreak
()¶ A routine that does nothing. This is called in place of IPyBreak and pdbBreak except when the debug option is set True in config.py
-
GSASIIpath.
IPyBreak_base
(userMsg=None)[source]¶ A routine that invokes an IPython session at the calling location This routine is only used when debug=True is set in config.py
-
GSASIIpath.
LoadConfigFile
(filename)[source]¶ Read a GSAS-II configuration file. Comments (starting with “%”) are removed, as are empty lines
Parameters: filename (str) – base file name (such as ‘file.dat’). Files with this name are located from the path and the contents of each are concatenated. Returns: a list containing each non-empty (after removal of comments) line found in every matching config file.
-
GSASIIpath.
MacRunScript
(script)[source]¶ Start a bash script in a new terminal window. Used on Mac OS X only.
Parameters: script (str) – file name for a bash script
-
GSASIIpath.
MacStartGSASII
(g2script, project='')[source]¶ Start a new instance of GSAS-II by opening a new terminal window and starting a new GSAS-II process. Used on Mac OS X only.
Parameters: - g2script (str) – file name for the GSASII.py script
- project (str) – GSAS-II project (.gpx) file to be opened, default is blank which opens a new project
-
GSASIIpath.
MakeByte2str
(arg)[source]¶ Convert output from subprocess pipes (bytes) to str (unicode) in Python 3. In Python 2: Leaves output alone (already str). Leaves stuff of other types alone (including unicode in Py2) Works recursively for string-like stuff in nested loops and tuples.
typical use:
out = MakeByte2str(out)
or:
out,err = MakeByte2str(s.communicate())
-
GSASIIpath.
SetBinaryPath
(printInfo=False, loadBinary=True)[source]¶ Add location of GSAS-II shared libraries (binaries: .so or .pyd files) to path
This routine must be executed after GSASIIpath is imported and before any other GSAS-II imports are done.
-
GSASIIpath.
SetConfigValue
(parmdict)[source]¶ Set configuration variables from a dictionary where elements are lists First item in list is the default value and second is the value to use.
-
GSASIIpath.
SetVersionNumber
(RevString)[source]¶ Set the subversion version number
Parameters: RevString (str) – something like “$Revision: 5438 $” that is set by subversion when the file is retrieved from subversion. Place
GSASIIpath.SetVersionNumber("$Revision: 5438 $")
in every python file.
-
GSASIIpath.
addCondaPkg
()[source]¶ Install the conda API into the current conda environment using the command line, so that the API can be used in the current Python interpreter
Attempts to do this without a shell failed on the Mac because it seems that the environment was inherited; seems to work w/o shell on Windows.
-
GSASIIpath.
addPrevGPX
(fil, configDict)[source]¶ Add a GPX file to the list of previous files. Move previous names to start of list. Keep most recent five files
-
GSASIIpath.
commonPath
(dir1, dir2)[source]¶ Check if two directories share a path. Note that paths are considered the same if either directory is a subdirectory of the other, but not if they are in different subdirectories /a/b/c shares a path with /a/b/c/d but /a/b/c/d and /a/b/c/e do not.
Returns: True if the paths are common
-
GSASIIpath.
condaEnvCreate
(envname, packageList, force=False)[source]¶ Create a Python interpreter in a new conda environment. Use this when there is a potential conflict between packages and it would be better to keep the packages separate (which is one of the reasons conda supports environments). Note that conda should be run from the case environment; this attempts to deal with issues if it is not.
Parameters: - envname (str) – the name of the environment to be created. If the environment exists, it will be overwritten only if force is True.
- packageList (list) –
a list of conda install create command options, such as:
['python=3.7', 'conda', 'gsl', 'diffpy.pdffit2', '-c', 'conda-forge', '-c', 'diffpy']
- force (bool) – if False (default) an error will be generated if an environment exists
Returns: (status,msg) where status is True if an error occurs and msg is a string with error information if status is True or the location of the newly-created Python interpreter.
-
GSASIIpath.
condaInstall
(packageList)[source]¶ Installs one or more packages using the anaconda conda package manager. Can be used to install multiple packages and optionally use channels.
Parameters: packageList (list) – a list of strings with name(s) of packages and optionally conda options. Examples:
packageList=['gsl'] packageList=['-c','conda-forge','wxpython'] packageList=['numpy','scipy','matplotlib']
Returns: None if the the command ran normally, or an error message if it did not.
-
GSASIIpath.
condaTest
(requireAPI=False)[source]¶ Returns True if it appears that Python is being run under Anaconda Python with conda present. Tests for conda environment vars and that the conda package is installed in the current environment.
Returns: True, if running under Conda
-
GSASIIpath.
exceptHook
(*args)[source]¶ A routine to be called when an exception occurs. It prints the traceback with fancy formatting and then calls an IPython shell with the environment of the exception location.
This routine is only used when debug=True is set in config.py
-
GSASIIpath.
findConda
()[source]¶ Determines if GSAS-II has been installed as g2conda or gsas2full with conda located relative to this file. We could also look for conda relative to the python (sys.executable) image, but I don’t want to muck around with python that someone else installed.
-
GSASIIpath.
fullsplit
(fil, prev=None)[source]¶ recursive routine to split all levels of directory names
-
GSASIIpath.
g2home
= 'https://subversion.xray.aps.anl.gov/pyGSAS'¶ Define the location of the GSAS-II subversion repository
-
GSASIIpath.
getsvnProxy
()[source]¶ Loads a proxy for subversion from the proxyinfo.txt file created by bootstrap.py or File => Edit Proxy…; If not found, then the standard http_proxy and https_proxy environment variables are scanned (see https://docs.python.org/3/library/urllib.request.html#urllib.request.getproxies) with case ignored and that is used.
-
GSASIIpath.
pdbBreak
()¶ A routine that does nothing. This is called in place of IPyBreak and pdbBreak except when the debug option is set True in config.py
-
GSASIIpath.
pipInstall
(packageList)[source]¶ Installs one or more packages using the pip package installer. Use of this should be avoided if conda can be used (see
condaTest()
to test for conda). Can be used to install multiple packages together. One can use pip options, but this is probably not needed.Parameters: packageList (list) – a list of strings with name(s) of packages Examples:
packageList=['gsl'] packageList=['wxpython','matplotlib','scipy'] packageList=[r'\Mac\Home\Scratch\wheels\pygsl-2.3.3-py3-none-any.whl'] packageList=['z:/Scratch/wheels/pygsl-2.3.3-py3-none-any.whl']
Returns: None if the the command ran normally, or an error message if it did not.
-
GSASIIpath.
proxycmds
= []¶ Used to hold proxy information for subversion, set if needed in whichsvn
-
GSASIIpath.
runScript
(cmds=[], wait=False, G2frame=None)[source]¶ run a shell script of commands in an external process
Parameters: - cmds (list) – a list of str’s, each ietm containing a shell (cmd.exe or bash) command
- wait (bool) – if True indicates the commands should be run and then the script should return. If False, then the currently running Python will exit. Default is False
- G2frame (wx.Frame) – provides the location of the current .gpx file to be used to restart GSAS-II after running the commands, if wait is False. Default is None which prevents restarting GSAS-II regardless of the value of wait.
-
GSASIIpath.
svnChecksumPatch
(svn, fpath, verstr)[source]¶ This performs a fix when svn cannot finish an update because of a Checksum mismatch error. This seems to be happening on OS X for unclear reasons.
-
GSASIIpath.
svnCleanup
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest', verbose=True)[source]¶ This runs svn cleanup on a selected local directory.
Parameters: fpath (str) – path to repository dictionary, defaults to directory where the current file is located
-
GSASIIpath.
svnFindLocalChanges
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest')[source]¶ - Returns a list of files that were changed locally. If no files are changed,
- the list has length 0
Parameters: fpath – path to repository dictionary, defaults to directory where the current file is located Returns: None if there is a subversion error (likely because the path is not a repository or svn is not found)
-
GSASIIpath.
svnGetFileStatus
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest', version=None)[source]¶ Compare file status to repository (svn status -u)
Returns: updatecount,modcount,locked where updatecount is the number of files waiting to be updated from repository modcount is the number of files that have been modified locally locked is the number of files tagged as locked
-
GSASIIpath.
svnGetLog
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest', version=None)[source]¶ Get the revision log information for a specific version of the specified package
Parameters: - fpath (str) – path to repository dictionary, defaults to directory where the current file is located.
- version (int) – the version number to be looked up or None (default) for the latest version.
Returns: a dictionary with keys (one hopes) ‘author’, ‘date’, ‘msg’, and ‘revision’
-
GSASIIpath.
svnGetRev
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest', local=True)[source]¶ Obtain the version number for the either the last update of the local version or contacts the subversion server to get the latest update version (# of Head).
Parameters: - fpath (str) – path to repository dictionary, defaults to directory where the current file is located
- local (bool) – determines the type of version number, where True (default): returns the latest installed update False: returns the version number of Head on the server
Returns: the version number as an str or None if there is a subversion error (likely because the path is not a repository or svn is not found). The error message is placed in global variable svnLastError
-
GSASIIpath.
svnInstallDir
(URL, loadpath)[source]¶ Load a subversion tree into a specified directory
Parameters: - URL (str) – the repository URL
- loadpath (str) – path to locate files
-
GSASIIpath.
svnLocCache
= None¶ Cached location of svn to avoid multiple searches for it
-
GSASIIpath.
svnSwitch2branch
(branch=None, loc=None, svnHome=None)[source]¶ Switch to a subversion branch if specified. Switches to trunk otherwise.
-
GSASIIpath.
svnSwitchDir
(rpath, filename, baseURL, loadpath=None, verbose=True)[source]¶ This performs a switch command to move files between subversion trees. Note that if the files were previously downloaded, the switch command will update the files to the newest version.
Parameters: - rpath (str) – path to locate files, relative to the GSAS-II installation path (defaults to path2GSAS2)
- URL (str) – the repository URL
- loadpath (str) – the prefix for the path, if specified. Defaults to path2GSAS2
- verbose (bool) – if True (default) diagnostics are printed
-
GSASIIpath.
svnUpdateDir
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest', version=None, verbose=True)[source]¶ This performs an update of the files in a local directory from a server.
Parameters: - fpath (str) – path to repository dictionary, defaults to directory where the current file is located
- version – the number of the version to be loaded. Used only cast as a string, but should be an integer or something that corresponds to a string representation of an integer value when cast. A value of None (default) causes the latest version on the server to be used.
-
GSASIIpath.
svnUpdateProcess
(version=None, projectfile=None, branch=None)[source]¶ perform an update of GSAS-II in a separate python process
-
GSASIIpath.
svnUpgrade
(fpath='/home/docs/checkouts/readthedocs.org/user_builds/gsas-ii/checkouts/latest')[source]¶ This reformats subversion files, which may be needed if an upgrade of subversion is done.
Parameters: fpath (str) – path to repository dictionary, defaults to directory where the current file is located
-
GSASIIpath.
svnVersion
(svn=None)[source]¶ Get the version number of the current subversion executable
Returns: a string with a version number such as “1.6.6” or None if subversion is not found.
4.2. GSASIIlog: Logging of “Actions”¶
Module to provide logging services, e.g. track and replay “actions” such as menu item, tree item, button press, value change and so on.
This capability is not currently implemented, but might be resurrected in some future version of GSAS-II.
-
GSASIIlog.
ButtonBindingLookup
= {}¶ Lookup table for button objects
-
GSASIIlog.
G2logList
= [None]¶ Contains a list of logged actions; first item is ignored
-
GSASIIlog.
InvokeMenuCommand
(id, G2frame, event)[source]¶ Called when a menu item is used to log the action as well as call the routine “bind”ed to that menu item
-
class
GSASIIlog.
LogEntry
[source]¶ Base class to define logging objects. These store information on events in a manner that can be pickled and saved – direct references to wx objects is not allowed.
Each object must define:
- __init__: stores the information needed to log & later recreate the action
- __str__ : shows a nice ASCII string for each action
- Replay: recreates the action when the log is played
optional:
- Repaint: redisplays the current window
-
GSASIIlog.
LogInfo
= {'LastPaintAction': None, 'Logging': False, 'Tree': None}¶ Contains values that are needed in the module for past actions & object location
-
GSASIIlog.
MenuBindingLookup
= {}¶ Lookup table for Menu buttons
-
class
GSASIIlog.
MenuLogEntry
(menulabellist)[source]¶ object that tracks when a menu command is executed
-
GSASIIlog.
OnReplayPress
(event)[source]¶ execute one or more commands when the replay button is pressed
-
GSASIIlog.
SaveMenuCommand
(id, G2frame, handler)[source]¶ Creates a table of menu items and their pseudo-bindings
-
class
GSASIIlog.
TabLogEntry
(title, tabname)[source]¶ Object to track when tabs are pressed in the DataFrame window
-
class
GSASIIlog.
TreeLogEntry
(itemlist)[source]¶ Object to track when tree items are pressed in the main window
-
class
GSASIIlog.
VarLogEntry
(treeRefs, indexRefs, value)[source]¶ object that tracks changes to a variable
-
class
GSASIIlog.
dictLogged
(obj, treeRefs, indexRefs=[])[source]¶ A version of a dict object that tracks the source of the object back to the location on the G2 tree. If a list (tuple) or dict are pulled from inside this object the source information is appended to the provinance tracking lists.
tuples are converted to lists.
-
class
GSASIIlog.
listLogged
(obj, treeRefs, indexRefs=[])[source]¶ A version of a list object that tracks the source of the object back to the location on the G2 tree. If a list (tuple) or dict are pulled from inside this object the source information is appended to the provinance tracking lists.
tuples are converted to lists.
4.3. config_example.py: Configuration options¶
This file contains optional configuration options for GSAS-II. The variables
in this file can be copied to file config.py, which is imported if present.
Access these variables using GSASIIpath.GetConfigValue()
, which returns
None if the variable is not set. Note that a config.py file need not
be present, but if in use it will typically be found with the GSAS-II source
directory (GSASIIpath.Path2GSAS2) or a directory for local GSAS-II
modifications (~/.G2local/ or /Documents and Settings/<User>/.G2local/).
Note that the contents of config.py is usually changed
using GSASIIctrlGUI.SelectConfigSetting.
When defining new config variables for GSAS-II, define them here with a default value: use None or a string for strings, or use integers or real values. Include a doc string after each variable is defined to explain what it does. Use names ending in _location or _directory for items that will contain directory names. Use names ending in _exec for executable files (.exe on windows).
For example:
test_int = 0
test_float = 0.0
test_string = None (or)
test_string = 'value'
-
config_example.
Arc_mask_azimuth
= 10.0¶ Specifies the default azimuthal range for creation of arc masks. Default is 10.0 degrees 2-theta.
-
config_example.
Autoint_PollTime
= 30.0¶ Specifies the frequency, in seconds that AutoInt checks for new files. Default is 30 seconds
-
config_example.
Autoscale_ParmNames
= ['userComment2', 'extraInputs\\1\\extraInputs', 'Ion_Chamber_I0']¶ Gives the possible selection of incident monitor names as found in an image metadata file. Used in AutoIntegration
-
config_example.
Clip_on
= True¶ if True then line plots willl be clipped at plot border; if False line plots extend nto white space around plot frme
-
config_example.
Column_Metadata_directory
= None¶ When specified and when images are read, GSAS-II will read metadata from a 1-ID style .par and a .EXT_lbls (EXT = image extension) or .lbls file. See
GSASIIfiles.readColMetadata()
for information on how this is done.
-
config_example.
Contour_color
= 'GSPaired'¶ Specifies the color map to be used for contour plots (images, pole figures, etc.) will be applied for new images and if Saved for a new start of GSAS-II
-
config_example.
DefaultAutoScale
= 'userComment2'¶ DefaultAutoScale selects one of the AutoScale_ParmNames. Used in AutoIntegration
-
config_example.
DrawAtoms_default
= ''¶ Allows selection of the default plotting mode for structures in Draw Atoms. The only valid values are: ‘lines’, ‘vdW balls’, ‘sticks’, ‘balls & sticks’, ‘ellipsoids’. %% If a non-valid choice is used (the default) ‘vdW balls’ is used.
-
config_example.
Enable_logging
= False¶ Set to True to enable use of command logging (under development.)
-
config_example.
G2RefinementWindow
= False¶ When True a custom progress window is displayed to track the progress of refinements. When False a generic wxpython supplied progress dialog is used.
-
config_example.
Help_mode
= 'browser'¶ Set to “internal” to use a Python-based web viewer to display help documentation and tutorials. If set to the default (“browser”) the default web browser is used.
-
config_example.
Image_2theta_max
= 50.0¶ Specifies a default 2-theta maximum used for calibration and integration as the Outer 2-theta value. Will be applied for newly-read images, but if changed the new value will be saved.
-
config_example.
Image_2theta_min
= 5.0¶ Specifies a default 2-theta minimum used for calibration and integration as the Inner 2-theta value. Will be applied for newly-read images, but if changed the new value will be saved.
-
config_example.
Image_calibrant
= ''¶ Specifies a default calibrant material for images. Will be applied for newly-read images, but if changed the specified material will be saved.
-
config_example.
Import_directory
= None¶ Specifies a default location for importing (reading) input files. Will be updated if Save_paths is True. Note that os.path.expanduser is run on this before it is used, so the user’s home directory can be specified with a ‘~’.
-
config_example.
Instprm_default
= False¶ when True, GSAS-II instprm file are shown as default; when False, old GSAS stype prm, etc files are default
-
config_example.
Main_Pos
= '(100,100)'¶ Main window location - will be updated & saved when user moves it. If position is outside screen then it will be repositioned to default
-
config_example.
Main_Size
= '(700,450)'¶ Main window size (width, height) - initially uses wx.DefaultSize but will updated and saved as the user changes the window
-
config_example.
Movie_fps
= 10¶ Specifies movie frames-per-second; larger number will make smoother modulation movies but larger files.
-
config_example.
Movie_time
= 5¶ Specifices time in sec for one modulation loop; larger number will give more frames for same fps’
-
config_example.
Multiprocessing_cores
= 0¶ Specifies the number of cores to use when performing multicore computing. A number less than zero causes the recommended number of cores [using multiprocessing.cpu_count()/2] to be used. Setting this number to 0 or 1 avoids use of the multiprocessing module: all computations are performed in-line.
-
config_example.
PDF_Rmax
= 100.0¶ Maximum radius for G(r) calculations: range is from 10-200A; default is 100A
-
config_example.
Plot_Colors
= 'k r g b m c'¶ The colors for line plots: use one of ‘k’-black, ‘r’-red, ‘b’-blue, ‘g’-green, ‘m’-magenta, ‘c’-cyan for the line colors in order of obs., calc., back., diff., color5 & color6 separated by spaces; 6 items required.
-
config_example.
Plot_Pos
= '(200,200)'¶ Plot window location - will be updated & saved when user moves it these widows. If position is outside screen then it will be repositioned to default
-
config_example.
Plot_Size
= '(700,600)'¶ Plot window size (width, height) - initially uses wx.DefaultSize but will updated and saved as the user changes the window
-
config_example.
Ring_mask_thickness
= 0.1¶ Specifies the default thickness for creation of ring and arc masks. Default is 0.1 degrees 2-theta.
-
config_example.
Save_paths
= False¶ When set to True, the last-used path for saving of .gpx and for importing of input files is saved in the configuration file. Note that since this causes the config.py file to be updated whenever files are saved/imported, any temporary config settings can be saved to disk at that point.
-
config_example.
SeparateHistPhaseTreeItem
= False¶ When this is set to True, the parameters for each histogram in each phase are placed in a separate 1st-level tree item rather than in the Data tab for each phase. Requires GSAS-II be restarted to take effect. Default is False.
This option is under development and is not fully tested.
-
config_example.
Show_timing
= False¶ If True, shows various timing results.
-
config_example.
Spot_mask_diameter
= 1.0¶ Specifies the default diameter for creation of spot masks. Default is 1.0 mm
-
config_example.
Starting_directory
= None¶ Specifies a default location for starting GSAS-II and where .gpx files should be read from. Will be updated if Save_paths is True. Note that os.path.expanduser is run on this before it is used, so the user’s home directory can be specified with a ‘~’.
-
config_example.
Tick_length
= 8.0¶ Specifies the length of phase tick marks in pixels. Default is 8.
-
config_example.
Tick_width
= 1.0¶ Specifies the width of phase tick marks in pixels. Fractional values do seem to produce an effect. Default is 1.
-
config_example.
Transpose
= False¶ Set to True to cause images to be Transposed when read (for code development)
-
config_example.
Tutorial_location
= None¶ Change this to place tutorials by in a different spot. If None, this defaults to <user>/My Documents/G2tutorials (on windows) or <user>/G2tutorials. If you want to use a different location, this can be set here. To install into the location where GSAS-II is installed, use this:
Tutorial_location = GSASIIpath.path2GSAS2
As another example, to use ~/.G2tutorials do this:
Tutorial_location = '~/.G2tutorials'
Note that os.path.expanduser is run on Tutorial_location before it is used. Also note that GSASIIpath is imported inside config.py; other imports should be avoided.
-
config_example.
debug
= False¶ Set to True to turn on debugging mode. This enables use of IPython on exceptions and on calls to
GSASIIpath.IPyBreak()
or breakpoint(). Calls toGSASIIpath.pdbBreak()
will invoke pdb at that location. %% If debug is False, calls toGSASIIpath.IPyBreak()
, breakpoint() andGSASIIpath.pdbBreak()
are ignored. %% From inside Spyder, calls to breakpoint() invoke the Spyder debugger, independent of the setting of debug. %% Restart GSAS-II for the setting of debug to take effect.
-
config_example.
enum_DrawAtoms_default
= ['', 'lines', 'vdW balls', 'sticks', 'balls & sticks', 'ellipsoids']¶ choices for DrawAtoms_default
-
config_example.
fullIntegrate
= True¶ If True then full image integration is default; False otherwise
-
config_example.
fullrmc_exec
= None¶ Defines the full path to a Python executable that has been configured with the fullrmc package. If None (the default), GSAS-II will see if fullrmc can be imported into the current Python and if not a executable named fullrmc* (or fullrmc*.exe on Windows) can be found in the GSAS-II binary directory or in the system path.
-
config_example.
lastUpdateNotice
= 0¶ Defines the version number for the last update notice that has been shown. This should not need to be changed manually.
-
config_example.
logging_debug
= False¶ Set to True to enable debug for logging (under development.)
-
config_example.
pdffit2_exec
= None¶ Defines the full path to a Python executable that has been configured with the PDFfit2 (diffpy) package. If None (the default), GSAS-II will see if PDFfit2 can be imported into the current Python.
-
config_example.
previous_GPX_files
= []¶ A list of previously used .gpx files
-
config_example.
show_gpxSize
= False¶ When True, the sizes of the sections of the GPX file are listed when the GPX file is opened. Default is False.
-
config_example.
svn_exec
= None¶ Defines the full path to a subversion executable. If None (the default), GSAS-II will search for a svn or svn.exe file in the current path or in the location where the current Python is located.
-
config_example.
wxInspector
= False¶ If set to True, the wxInspector widget is displayed when GSAS-II is started.
4.4. GSASIIElem: functions for element types¶
-
GSASIIElem.
CheckElement
(El)[source]¶ Check if element El is in the periodic table
Parameters: El (str) – One or two letter element symbol, capitaliztion ignored Returns: True if the element is found
-
GSASIIElem.
ComptonFac
(El, SQ)[source]¶ compute Compton scattering factor
Parameters: - El – element dictionary
- SQ – (sin-theta/lambda)**2
Returns: compton scattering factor
-
GSASIIElem.
FPcalc
(Orbs, KEv)[source]¶ Compute real & imaginary resonant X-ray scattering factors
Parameters: - Orbs – list of orbital dictionaries as defined in GetXsectionCoeff
- KEv – x-ray energy in keV
Returns: C: (f’,f”,mu): real, imaginary parts of resonant scattering & atomic absorption coeff.
-
GSASIIElem.
GetBLtable
(General)[source]¶ returns a dictionary of neutron scattering length data for atom types & isotopes found in General
Parameters: General (dict) – dictionary of phase info.; includes AtomTypes & Isotopes Returns: BLtable, dictionary of scattering length data; key is atom type
-
GSASIIElem.
GetEFFtable
(atomTypes)[source]¶ returns a dictionary of electron form factor data for atom types found in atomTypes might not be needed?
Parameters: atomTypes (list) – list of atom types Returns: FFtable, dictionary of form factor data; key is atom type
-
GSASIIElem.
GetEFormFactorCoeff
(El)[source]¶ Read electron form factor coefficients from atomdata.py file
Parameters: El (str) – element 1-2 character symbol, case irrevelant Returns: FormFactors: list of form factor dictionaries Each electrn form factor dictionary is:
- Symbol: 4 character element symbol (no valence)
- Z: atomic number
- fa: 5 A coefficients
- fb: 5 B coefficients
-
GSASIIElem.
GetFFC5
(ElSym)[source]¶ Get 5 term form factor and Compton scattering data
Parameters: ElSym – str(1-2 character element symbol with proper case); Return El: dictionary with 5 term form factor & compton coefficients
-
GSASIIElem.
GetFFtable
(atomTypes)[source]¶ returns a dictionary of form factor data for atom types found in atomTypes
Parameters: atomTypes (list) – list of atom types Returns: FFtable, dictionary of form factor data; key is atom type
-
GSASIIElem.
GetFormFactorCoeff
(El)[source]¶ Read X-ray form factor coefficients from atomdata.py file
Parameters: El (str) – element 1-2 character symbol, case irrevelant Returns: FormFactors: list of form factor dictionaries Each X-ray form factor dictionary is:
- Symbol: 4 character element symbol with valence (e.g. ‘NI+2’)
- Z: atomic number
- fa: 4 A coefficients
- fb: 4 B coefficients
- fc: C coefficient
-
GSASIIElem.
GetMFtable
(atomTypes, Landeg)[source]¶ returns a dictionary of magnetic form factor data for atom types found in atomTypes
Parameters: - atomTypes (list) – list of atom types
- Landeg (list) – Lande g factors for atomTypes
Returns: FFtable, dictionary of form factor data; key is atom type
-
GSASIIElem.
GetMagFormFacCoeff
(El)[source]¶ Read magnetic form factor data from atmdata.py
Parameters: El – 2 character element symbol Returns: MagFormFactors: list of all magnetic form factors dictionaries for element El. each dictionary contains:
- ‘Symbol’:Symbol
- ‘Z’:Z
- ‘mfa’: 4 MA coefficients
- ‘nfa’: 4 NA coefficients
- ‘mfb’: 4 MB coefficients
- ‘nfb’: 4 NB coefficients
- ‘mfc’: MC coefficient
- ‘nfc’: NC coefficient
-
GSASIIElem.
GetXsectionCoeff
(El)[source]¶ Read atom orbital scattering cross sections for fprime calculations via Cromer-Lieberman algorithm
Parameters: El – 2 character element symbol Returns: Orbs: list of orbitals each a dictionary with detailed orbital information used by FPcalc each dictionary is:
- ‘OrbName’: Orbital name read from file
- ‘IfBe’ 0/2 depending on orbital
- ‘BindEn’: binding energy
- ‘BB’: BindEn/0.02721
- ‘XSectIP’: 5 cross section inflection points
- ‘ElEterm’: energy correction term
- ‘SEdge’: absorption edge for orbital
- ‘Nval’: 10/11 depending on IfBe
- ‘LEner’: 10/11 values of log(energy)
- ‘LXSect’: 10/11 values of log(cross section)
-
GSASIIElem.
MagScatFac
(El, SQ)[source]¶ compute value of form factor
Parameters: - El – element dictionary defined in GetFormFactorCoeff
- SQ – (sin-theta/lambda)**2
- gfac – Lande g factor (normally = 2.0)
Returns: real part of form factor
-
GSASIIElem.
ScatFac
(El, SQ)[source]¶ compute value of form factor
Parameters: - El – element dictionary defined in GetFormFactorCoeff
- SQ – (sin-theta/lambda)**2
Returns: real part of form factor
4.5. GSASIIlattice: Unit cells¶
Perform lattice-related computations
Note that G is the reciprocal lattice tensor, and g is its inverse, \(G = g^{-1}\), where
\[\begin{split}g = \left( \begin{matrix} a^2 & a b\cos\gamma & a c\cos\beta \\ a b\cos\gamma & b^2 & b c \cos\alpha \\ a c\cos\beta & b c \cos\alpha & c^2 \end{matrix}\right)\end{split}\]
The “A tensor” terms are defined as
\(A = (\begin{matrix} G_{11} & G_{22} & G_{33} & 2G_{12} & 2G_{13} & 2G_{23}\end{matrix})\) and A can be used in this fashion:
\(d^* = \sqrt {A_0 h^2 + A_1 k^2 + A_2 l^2 + A_3 hk + A_4 hl + A_5 kl}\), where
d is the d-spacing, and \(d^*\) is the reciprocal lattice spacing,
\(Q = 2 \pi d^* = 2 \pi / d\).
Note that GSAS-II variables p::Ai
(i = 0, 1,… 5) and p
is a phase number are
used for the Ai values. See A2cell()
, cell2A()
for interconversion between A and
unit cell parameters; cell2Gmat()
Gmat2cell()
for G and cell parameters.
When the hydrostatic/elastic strain coefficients (Dij, \(D_{ij}\)) are used, they are added to the
A tensor terms (Ai, \(A_{i}\)) so that A is redefined
\(A = (\begin{matrix} A_{0} + D_{11} & A_{1} + D_{22} & A_{2} + D_{33} & A_{3} + D_{12} & A_{4} + D_{13} & A_{5} + D_{23}\end{matrix})\). See cellDijFill()
.
Note that GSAS-II variables p:h:Dij
(i,j = 1, 2, 3) and p
is a phase number
and h
a histogram number are used for the Dij values.
-
GSASIIlattice.
A2Gmat
(A, inverse=True)[source]¶ Fill real & reciprocal metric tensor (G) from A.
Parameters: - A – reciprocal metric tensor elements as [G11,G22,G33,2*G12,2*G13,2*G23]
- inverse (bool) – if True return both G and g; else just G
Returns: reciprocal (G) & real (g) metric tensors (list of two numpy 3x3 arrays)
-
GSASIIlattice.
A2cell
(A)[source]¶ Compute unit cell constants from A
Parameters: A – [G11,G22,G33,2*G12,2*G13,2*G23] G - reciprocal metric tensor Returns: a,b,c,alpha, beta, gamma (degrees) - lattice parameters
-
GSASIIlattice.
A2invcell
(A)[source]¶ Compute reciprocal unit cell constants from A returns tuple with a*,b*,c*,alpha*, beta*, gamma* (degrees)
-
GSASIIlattice.
AplusDij
(A, Dij, SGData)[source]¶ returns the A corrected by Dij
Parameters: - A (list) – reciprocal metric terms A0-A5
- Dij (array) – unique Dij values as stored in Hstrain
- SGdata (dict) – a symmetry object
Returns list newA: A corrected by Dij
-
GSASIIlattice.
CellAbsorption
(ElList, Volume)[source]¶ Compute unit cell absorption
Parameters: - ElList (dict) – dictionary of element contents including mu and number of atoms be cell
- Volume (float) – unit cell volume
Returns: mu-total/Volume
-
GSASIIlattice.
CellBlock
(nCells)[source]¶ Generate block of unit cells n*n*n on a side; [0,0,0] centered, n = 2*nCells+1 currently only works for nCells = 0 or 1 (not >1)
-
GSASIIlattice.
CellDijCorr
(Cell, SGData, Data, hist)[source]¶ Returns the cell corrected for Dij values.
Parameters: - Cell (list) – lattice parameters
- SGdata (dict) – a symmetry object
- Data (dict) – phase data structure; contains set of Dij values
- hist (str) – histogram name
Returns: cell corrected for Dij values
-
GSASIIlattice.
CosAngle
(U, V, G)[source]¶ calculate cos of angle between U & V in generalized coordinates defined by metric tensor G
Parameters: - U – 3-vectors assume numpy arrays, can be multiple reflections as (N,3) array
- V – 3-vectors assume numpy arrays, only as (3) vector
- G – metric tensor for U & V defined space assume numpy array
Returns: cos(phi)
-
GSASIIlattice.
CosSinAngle
(U, V, G)[source]¶ calculate sin & cos of angle between U & V in generalized coordinates defined by metric tensor G
Parameters: - U – 3-vectors assume numpy arrays
- V – 3-vectors assume numpy arrays
- G – metric tensor for U & V defined space assume numpy array
Returns: cos(phi) & sin(phi)
-
GSASIIlattice.
CubicSHarm
(L, M, Th, Ph)[source]¶ Calculation of the cubic harmonics given in Table 3 in M.Kara & K. Kurki-Suonio, Acta Cryt. A37, 201 (1981). For L = 14,20 only for m3m from F.M. Mueller and M.G. Priestley, Phys Rev 148, 638 (1966)
Parameters: - L (int) – degree of the harmonic (L >= 0)
- M (int) – order number [|M| <= L]
- Th (float/array) – Azimuthal coordinate 0 <= Th <= 360
- Ph (float/array) – Polar coordinate 0<= Ph <= 180
Returns klm value/array: cubic harmonics
-
GSASIIlattice.
Dsp2pos
(Inst, dsp)[source]¶ convert d-spacing to powder pattern position (2-theta or TOF, musec)
-
GSASIIlattice.
FindNonstandard
(controls, Phase)[source]¶ Find nonstandard setting of magnetic cell that aligns with parent nuclear cell
Parameters: - controls – list unit cell indexing controls
- Phase – dict new magnetic phase data (NB:not G2 phase construction); modified here
Returns: None
-
GSASIIlattice.
GenCellConstraints
(Trans, origPhase, newPhase, origA, oSGLaue, nSGLaue, debug=False)[source]¶ Generate the constraints between two unit cells constants for a phase transformed by matrix Trans.
Parameters: - Trans (np.array) – a 3x3 direct cell transformation matrix where, Trans = np.array([ [2/3, 4/3, 1/3], [-1, 0, 0], [-1/3, -2/3, 1/3] ]) (for a’ = 2/3a + 4/3b + 1/3c; b’ = -a; c’ = -1/3, -2/3, 1/3)
- origPhase (int) – phase id (pId) for original phase
- newPhase (int) – phase id for the transformed phase to be constrained from original phase
- origA (list) – reciprocal cell (“A*”) tensor (used for debug only)
- oSGLaue (dict) – space group info for original phase
- nSGLaue (dict) – space group info for transformed phase
- debug (bool) – If true, the constraint input is used to compute and print A* and from that the direct cell for the transformed phase.
-
GSASIIlattice.
GenHBravais
(dmin, Bravais, A, cctbx_args=None)[source]¶ Generate the positionally unique powder diffraction reflections
Parameters: - dmin – minimum d-spacing in A
- Bravais –
lattice type (see GetBraviasNum). Bravais is one of:
- 0 F cubic
- 1 I cubic
- 2 P cubic
- 3 R hexagonal (trigonal not rhombohedral)
- 4 P hexagonal
- 5 I tetragonal
- 6 P tetragonal
- 7 F orthorhombic
- 8 I orthorhombic
- 9 A orthorhombic
- 10 B orthorhombic
- 11 C orthorhombic
- 12 P orthorhombic
- 13 I monoclinic
- 14 A monoclinic
- 15 C monoclinic
- 16 P monoclinic
- 17 P triclinic
- A – reciprocal metric tensor elements as [G11,G22,G33,2*G12,2*G13,2*G23]
- cctbx_args (dict) –
items defined in CCTBX:
- ’sg_type’: value from cctbx.sgtbx.space_group_type(symmorphic_sgs[ibrav])
- ’uctbx_unit_cell’: pointer to
cctbx.uctbx.unit_cell()
- ’miller_index_generator’: pointer to
cctbx.miller.index_generator()
Returns: HKL unique d list of [h,k,l,d,-1] sorted with largest d first
-
GSASIIlattice.
GenHLaue
(dmin, SGData, A)[source]¶ Generate the crystallographically unique powder diffraction reflections for a lattice and Bravais type
Parameters: - dmin – minimum d-spacing
- SGData –
space group dictionary with at least
- ’SGLaue’: Laue group symbol: one of ‘-1’,’2/m’,’mmm’,’4/m’,’6/m’,’4/mmm’,’6/mmm’, ‘3m1’, ‘31m’, ‘3’, ‘3R’, ‘3mR’, ‘m3’, ‘m3m’
- ’SGLatt’: lattice centering: one of ‘P’,’A’,’B’,’C’,’I’,’F’
- ’SGUniq’: code for unique monoclinic axis one of ‘a’,’b’,’c’ (only if ‘SGLaue’ is ‘2/m’) otherwise an empty string
- A – reciprocal metric tensor elements as [G11,G22,G33,2*G12,2*G13,2*G23]
Returns: HKL = list of [h,k,l,d] sorted with largest d first and is unique part of reciprocal space ignoring anomalous dispersion
-
GSASIIlattice.
GenPfHKLs
(nMax, SGData, A)[source]¶ Generate the unique pole figure reflections for a lattice and Bravais type. Min d-spacing=1.0A & no more than nMax returned
Parameters: - nMax – maximum number of hkls returned
- SGData –
space group dictionary with at least
- ’SGLaue’: Laue group symbol: one of ‘-1’,’2/m’,’mmm’,’4/m’,’6/m’,’4/mmm’,’6/mmm’, ‘3m1’, ‘31m’, ‘3’, ‘3R’, ‘3mR’, ‘m3’, ‘m3m’
- ’SGLatt’: lattice centering: one of ‘P’,’A’,’B’,’C’,’I’,’F’
- ’SGUniq’: code for unique monoclinic axis one of ‘a’,’b’,’c’ (only if ‘SGLaue’ is ‘2/m’) otherwise an empty string
- A – reciprocal metric tensor elements as [G11,G22,G33,2*G12,2*G13,2*G23]
Returns: HKL = list of ‘h k l’ strings sorted with largest d first; no duplicate zones
-
GSASIIlattice.
GenerateCellConstraints
()[source]¶ Generate unit cell constraints for transforming one set of A tensor values to another using symbolic math (requires the sympy package)
Note that this is only used to do the symbolic math needed to generate cell relationships. It is not used normally in GSAS-II.
-
GSASIIlattice.
GetBraviasNum
(center, system)[source]¶ Determine the Bravais lattice number, as used in GenHBravais
Parameters: - center – one of: ‘P’, ‘C’, ‘I’, ‘F’, ‘R’ (see SGLatt from GSASIIspc.SpcGroup)
- system – one of ‘cubic’, ‘hexagonal’, ‘tetragonal’, ‘orthorhombic’, ‘trigonal’ (for R) ‘monoclinic’, ‘triclinic’ (see SGSys from GSASIIspc.SpcGroup)
Returns: a number between 0 and 13 or throws a ValueError exception if the combination of center, system is not found (i.e. non-standard)
-
GSASIIlattice.
GetKclKsl
(L, N, SGLaue, psi, phi, beta)[source]¶ - This is used for spherical harmonics description of preferred orientation;
- cylindrical symmetry only (M=0) and no sample angle derivatives returned
-
GSASIIlattice.
Gmat2A
(G)[source]¶ Extract A from reciprocal metric tensor (G)
Parameters: G – reciprocal maetric tensor (3x3 numpy array Returns: A = [G11,G22,G33,2*G12,2*G13,2*G23]
-
GSASIIlattice.
Gmat2AB
(G)[source]¶ Computes orthogonalization matrix from reciprocal metric tensor G
Returns: tuple of two 3x3 numpy arrays (A,B) - A for crystal to Cartesian transformations (A*x = np.inner(A,x) = X)
- B (= inverse of A) for Cartesian to crystal transformation (B*X = np.inner(B,X) = x)
-
GSASIIlattice.
Gmat2cell
(g)[source]¶ Compute real/reciprocal lattice parameters from real/reciprocal metric tensor (g/G) The math works the same either way.
Parameters: (or G) (g) – real (or reciprocal) metric tensor 3x3 array Returns: a,b,c,alpha, beta, gamma (degrees) (or a*,b*,c*,alpha*,beta*,gamma* degrees)
-
GSASIIlattice.
HKL2SpAng
(H, cell, SGData)[source]¶ Computes spherical coords for hkls; view along 001
Parameters: - H (array) – arrays of hkl
- cell (tuple) – a,b,c, alpha, beta, gamma (degrees)
- SGData (dict) – space group dictionary
Returns: arrays of r,phi,psi (radius,inclination,azimuth) about 001
-
GSASIIlattice.
LaueUnique
(Laue, HKLF)[source]¶ Impose Laue symmetry on hkl
Parameters: - Laue (str) –
Laue symbol, as below
centrosymmetric Laue groups:
['-1','2/m','112/m','2/m11','mmm','-42m','-4m2','4/mmm','-3','-3m', '-31m','-3m1','6/m','6/mmm','m3','m3m']
noncentrosymmetric Laue groups:
['1','2','211','112','m','m11','11m','222','mm2','m2m','2mm', '4','-4','422','4mm','3','312','321','3m','31m','3m1','6','-6', '622','6mm','-62m','-6m2','23','432','-43m']
- HKLF – np.array([[h,k,l,…]]) reflection set to be converted
Returns: HKLF new reflection array with imposed Laue symmetry
- Laue (str) –
-
GSASIIlattice.
LaueUnique2
(SGData, refList)[source]¶ Impose Laue symmetry on hkl
Parameters: - SGData – space group data from ‘P ‘+Laue
- HKLF – np.array([[h,k,l,…]]) reflection set to be converted
Returns: HKLF new reflection array with imposed Laue symmetry
-
GSASIIlattice.
OdfChk
(SGLaue, L, M)[source]¶ finds symmetry rules for spherical harmonic coefficients for Laue groups :param str SGLaue: Laue symbol :param int L: principal harmonic term; only evens are used :param int M: second harmonic term; can be -L <= M <= L :returns True if allowed
-
GSASIIlattice.
PlaneIntercepts
(Amat, H, phase, stack)[source]¶ find unit cell intercepts for a stack of hkl planes
-
GSASIIlattice.
Pos2dsp
(Inst, pos)[source]¶ convert powder pattern position (2-theta or TOF, musec) to d-spacing is currently only approximate for EDX data; accurate for others.
-
GSASIIlattice.
RBChk
(sytsym, L, M)[source]¶ finds symmetry rules for spherical harmonic coefficients for site symmetries :param str SGLaue: Laue symbol or sytsym symbol :param int L: principal harmonic term; only evens are used :param int M: second harmonic term; can be -L <= M <= L :returns True if allowed and sign for term NB: not complete for all site symmetries! Many are missing
-
GSASIIlattice.
RBsymCheck
(Atoms, ct, cx, cs, AtLookUp, Amat, RBObjIds, SGData)[source]¶ Checks members of a rigid body to see if one is a symmetry equivalent of another. If so the atom site frac is set to zero.
Parameters: - Atoms – atom array as defined in GSAS-II; modified here
- ct – int location of atom type in Atoms item
- cx – int location of x,y,z,frac in Atoms item
- AtLookUp (dict) – atom lookup by Id table
- Amat (np.array) – crystal-to-Cartesian transformation matrix
- RBObjIds (list) – atom Id belonging to rigid body being tested
- SGData (dict) – GSAS-II space group info.
Returns: Atoms with modified atom frac entries
-
GSASIIlattice.
RBsymChk
(RBsym, coefNames)[source]¶ imposes rigid body symmetry on spherical harmonics terms Key problem is noncubic RB symmetries in cubic site symmetries & vice versa.
-
GSASIIlattice.
SHarmcal
(SytSym, SHFln, psi, gam)[source]¶ Perform a surface spherical harmonics computation. Note that the the number of gam values must either be 1 or must match psi
Parameters: - SytSym (str) – sit symmetry - only looking for cubics
- SHFln (dict) – spherical harmonics coefficients; key has L & M
- psi (float/array) – Azimuthal coordinate 0 <= Th <= 360
- gam (float/array) – Polar coordinate 0<= Ph <= 180
Returns array SHVal: spherical harmonics array for psi,gam values
-
GSASIIlattice.
SamAng
(Tth, Gangls, Sangl, IFCoup)[source]¶ Compute sample orientation angles vs laboratory coord. system
Parameters: - Tth – Signed theta
- Gangls – Sample goniometer angles phi,chi,omega,azmuth
- Sangl – Sample angle zeros om-0, chi-0, phi-0
- IFCoup – True if omega & 2-theta coupled in CW scan
Returns: psi,gam: Sample odf angles dPSdA,dGMdA: Angle zero derivatives
-
GSASIIlattice.
SphHarmAng
(L, M, P, Th, Ph)[source]¶ Compute spherical harmonics values using scipy.special.sph_harm
Parameters: - L (int) – degree of the harmonic (L >= 0)
- M (int) – order number (|M| <= L)
- P (int) – sign flag = -1 or 1
- Th (float/array) – Azimuthal coordinate 0 <= Th <= 360
- Ph (float/array) – Polar coordinate 0<= Ph <= 180
Returns ylmp value/array: as reals
-
GSASIIlattice.
TOF2dsp
(Inst, Pos)[source]¶ convert powder pattern TOF, musec to d-spacing by successive approximation Pos can be numpy array
-
GSASIIlattice.
TransformCell
(cell, Trans)[source]¶ Transform lattice parameters by matrix
Parameters: - cell – list a,b,c,alpha,beta,gamma,(volume)
- Trans – array transformation matrix
Returns: array transformed a,b,c,alpha,beta,gamma,volume
-
GSASIIlattice.
TransformPhase
(oldPhase, newPhase, Trans, Uvec, Vvec, ifMag, Force=True)[source]¶ Transform atoms from oldPhase to newPhase M’ is inv(M) does X’ = M(X-U)+V transformation for coordinates and U’ = MUM/det(M) for anisotropic thermal parameters
Parameters: - oldPhase – dict G2 phase info for old phase
- newPhase – dict G2 phase info for new phase; with new cell & space group atoms are from oldPhase & will be transformed
- Trans – lattice transformation matrix M
- Uvec – array parent coordinates transformation vector U
- Vvec – array child coordinate transformation vector V
- ifMag – bool True if convert to magnetic phase; if True all nonmagnetic atoms will be removed
Returns: newPhase dict modified G2 phase info
Returns: atCodes list atom transformation codes
-
GSASIIlattice.
U6toUij
(U6)[source]¶ Fill matrix (Uij) from U6 = [U11,U22,U33,U12,U13,U23] NB: there is a non numpy version in GSASIIspc: U2Uij
Parameters: U6 (list) – 6 terms of u11,u22,… Returns: Uij - numpy [3][3] array of uij
-
GSASIIlattice.
Uij2Ueqv
(Uij, GS, Amat)[source]¶ returns 1/3 trace of diagonalized U matrix :param Uij: numpy array [Uij] :param GS: Uij too betaij conversion matrix :param Amat: crystal to Cartesian transformation matrix :returns: 1/3 trace of diagonalized U matrix :returns: True if nonpositive-definate; False otherwise
-
GSASIIlattice.
Uij2betaij
(Uij, G)[source]¶ Convert Uij to beta-ij tensors – stub for eventual completion
Parameters: - Uij – numpy array [Uij]
- G – reciprocal metric tensor
Returns: beta-ij - numpy array [beta-ij]
-
GSASIIlattice.
UijtoU6
(U)[source]¶ Fill vector [U11,U22,U33,U12,U13,U23] from Uij NB: there is a non numpy version in GSASIIspc: Uij2U
-
GSASIIlattice.
UniqueCellByLaue
= [[['m3', 'm3m'], (0,)], [['3R', '3mR'], (0, 3)], [['3', '3m1', '31m', '6/m', '6/mmm', '4/m', '4/mmm'], (0, 2)], [['mmm'], (0, 1, 2)], [['2/ma'], (0, 1, 2, 3)], [['2/mb'], (0, 1, 2, 4)], [['2/mc'], (0, 1, 2, 5)], [['-1'], (0, 1, 2, 3, 4, 5)]]¶ List the unique cell terms by index for each Laue class
-
GSASIIlattice.
betaij2Uij
(betaij, G)[source]¶ Convert beta-ij to Uij tensors
:param beta-ij - numpy array [beta-ij] :param G: reciprocal metric tensor :returns: Uij: numpy array [Uij]
-
GSASIIlattice.
calc_rVsq
(A)[source]¶ Compute the square of the reciprocal lattice volume (1/V**2) from A’
-
GSASIIlattice.
cell2A
(cell)[source]¶ Obtain A = [G11,G22,G33,2*G12,2*G13,2*G23] from lattice parameters
Parameters: cell – [a,b,c,alpha,beta,gamma] (degrees) Returns: G reciprocal metric tensor as 3x3 numpy array
-
GSASIIlattice.
cell2AB
(cell, alt=False)[source]¶ Computes orthogonalization matrix from unit cell constants
Parameters: cell (tuple) – a,b,c, alpha, beta, gamma (degrees) Returns: tuple of two 3x3 numpy arrays (A,B) A for crystal to Cartesian transformations A*x = np.inner(A,x) = X B (= inverse of A) for Cartesian to crystal transformation B*X = np.inner(B,X) = x
-
GSASIIlattice.
cell2Gmat
(cell)[source]¶ Compute real and reciprocal lattice metric tensor from unit cell constants
Parameters: cell – tuple with a,b,c,alpha, beta, gamma (degrees) Returns: reciprocal (G) & real (g) metric tensors (list of two numpy 3x3 arrays)
-
GSASIIlattice.
cellAlbl
= ('a', 'b', 'c', 'alpha', 'beta', 'gamma')¶ ASCII labels for a, b, c, alpha, beta, gamma
-
GSASIIlattice.
cellDijFill
(pfx, phfx, SGData, parmDict)[source]¶ Returns the filled-out reciprocal cell (A) terms from the parameter dictionaries corrected for Dij.
Parameters: - pfx (str) – parameter prefix (“n::”, where n is a phase number)
- SGdata (dict) – a symmetry object
- parmDict (dict) – a dictionary of parameters
Returns: A,sigA where each is a list of six terms with the A terms
-
GSASIIlattice.
cellUlbl
= ('a', 'b', 'c', 'α', 'β', 'γ')¶ unicode labels for a, b, c, alpha, beta, gamma
-
GSASIIlattice.
cellUnique
(SGData)[source]¶ Returns the indices for the unique A tensor terms based on the Laue class. Any terms that are determined from others or are zero are not included.
Parameters: SGdata (dict) – a symmetry object Returns: a list of 0 to 6 terms with indices of the unique A terms
-
GSASIIlattice.
cellXformRelations
= {0: ['1.0*A0*T[0,0]**2', '1.0*A1*T[0,1]**2', '1.0*A2*T[0,2]**2', '1.0*A3*T[0,0]*T[0,1]', '1.0*A4*T[0,0]*T[0,2]', '1.0*A5*T[0,1]*T[0,2]'], 1: ['1.0*A0*T[1,0]**2', '1.0*A1*T[1,1]**2', '1.0*A2*T[1,2]**2', '1.0*A3*T[1,0]*T[1,1]', '1.0*A4*T[1,0]*T[1,2]', '1.0*A5*T[1,1]*T[1,2]'], 2: ['1.0*A0*T[2,0]**2', '1.0*A1*T[2,1]**2', '1.0*A2*T[2,2]**2', '1.0*A3*T[2,0]*T[2,1]', '1.0*A4*T[2,0]*T[2,2]', '1.0*A5*T[2,1]*T[2,2]'], 3: ['2.0*A0*T[0,0]*T[1,0]', '2.0*A1*T[0,1]*T[1,1]', '2.0*A2*T[0,2]*T[1,2]', '1.0*A3*(T[0,0]*T[1,1] + T[1,0]*T[0,1])', '1.0*A4*(T[0,0]*T[1,2] + T[1,0]*T[0,2])', '1.0*A5*(T[0,1]*T[1,2] + T[1,1]*T[0,2])'], 4: ['2.0*A0*T[0,0]*T[2,0]', '2.0*A1*T[0,1]*T[2,1]', '2.0*A2*T[0,2]*T[2,2]', '1.0*A3*(T[0,0]*T[2,1] + T[2,0]*T[0,1])', '1.0*A4*(T[0,0]*T[2,2] + T[2,0]*T[0,2])', '1.0*A5*(T[0,1]*T[2,2] + T[2,1]*T[0,2])'], 5: ['2.0*A0*T[1,0]*T[2,0]', '2.0*A1*T[1,1]*T[2,1]', '2.0*A2*T[1,2]*T[2,2]', '1.0*A3*(T[1,0]*T[2,1] + T[2,0]*T[1,1])', '1.0*A4*(T[1,0]*T[2,2] + T[2,0]*T[1,2])', '1.0*A5*(T[1,1]*T[2,2] + T[2,1]*T[1,2])']}¶ cellXformRelations provide the constraints on newA[i] values for a new cell generated from oldA[i] values.
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GSASIIlattice.
cellZeros
(SGData)[source]¶ Returns a list with the A terms required to be zero based on Laue symmetry
Parameters: SGdata (dict) – a symmetry object Returns: A list of six terms where the values are True if the A term must be zero, False otherwise.
-
GSASIIlattice.
criticalEllipse
(prob)[source]¶ Calculate critical values for probability ellipsoids from probability
-
GSASIIlattice.
fillgmat
(cell)[source]¶ Compute lattice metric tensor from unit cell constants
Parameters: cell – tuple with a,b,c,alpha, beta, gamma (degrees) Returns: 3x3 numpy array
-
GSASIIlattice.
fmtCellConstraints
(cellConstr)[source]¶ Format the cell relationships created in
GenerateCellConstraints()
in a format that can be used to generate constraints.Use:
cXforms = G2lat.fmtCellConstraints(G2lat.GenerateCellConstraints())
Note that this is only used to do the symbolic math needed to generate cell relationships. It is not used normally in GSAS-II.
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GSASIIlattice.
getPeakPos
(dataType, parmdict, dsp)[source]¶ convert d-spacing to powder pattern position (2-theta, E or TOF, musec)
-
GSASIIlattice.
invcell2Gmat
(invcell)[source]¶ - Compute real and reciprocal lattice metric tensor from reciprocal
- unit cell constants
Parameters: invcell – [a*,b*,c*,alpha*, beta*, gamma*] (degrees) Returns: reciprocal (G) & real (g) metric tensors (list of two 3x3 arrays)
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GSASIIlattice.
polfcal
(ODFln, SamSym, psi, gam)[source]¶ Perform a pole figure computation. Note that the the number of gam values must either be 1 or must match psi. Updated for numpy 1.8.0
-
GSASIIlattice.
prodMGMT
(G, Mat)[source]¶ Transform metric tensor by matrix
Parameters: - G – array metric tensor
- Mat – array transformation matrix
Returns: array new metric tensor
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GSASIIlattice.
rotdMat
(angle, axis=0)[source]¶ Prepare rotation matrix for angle in degrees about axis(=0,1,2)
Parameters: - angle – angle in degrees
- axis – axis (0,1,2 = x,y,z) about which for the rotation
Returns: rotation matrix - 3x3 numpy array
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GSASIIlattice.
rotdMat4
(angle, axis=0)[source]¶ Prepare rotation matrix for angle in degrees about axis(=0,1,2) with scaling for OpenGL
Parameters: - angle – angle in degrees
- axis – axis (0,1,2 = x,y,z) about which for the rotation
Returns: rotation matrix - 4x4 numpy array (last row/column for openGL scaling)
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GSASIIlattice.
sec2HMS
(sec)[source]¶ Convert time in sec to H:M:S string
Parameters: sec – time in seconds Returns: H:M:S string (to nearest 100th second)
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GSASIIlattice.
selftestlist
= []¶ Defines a list of self-tests
-
GSASIIlattice.
sortHKLd
(HKLd, ifreverse, ifdup, ifSS=False)[source]¶ sort reflection list on d-spacing; can sort in either order
Parameters: - HKLd – a list of [h,k,l,d,…];
- ifreverse – True for largest d first
- ifdup – True if duplicate d-spacings allowed
Returns: sorted reflection list
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GSASIIlattice.
subVals
(expr, A, T)[source]¶ Evaluate the symbolic expressions by substituting for A0-A5 & Tij
This can be used on the cell relationships created in
GenerateCellConstraints()
like this:Trans = np.array([ [2/3, 4/3, 1/3], [-1, 0, 0], [-1/3, -2/3, 1/3] ]) T = np.linalg.inv(Trans).T print([subVals(i,Aold,T) for i in GenerateCellConstraints()])
Parameters: - expr (list) – a list of sympy expressions.
- A (list) – This is the A* tensor as defined above.
- T (np.array) – a 3x3 transformation matrix where, Trans = np.array([ [2/3, 4/3, 1/3], [-1, 0, 0], [-1/3, -2/3, 1/3] ]) (for a’ = 2/3a + 4/3b + 1/3c; b’ = -a; c’ = -1/3, -2/3, 1/3) then T = np.linalg.inv(Trans).T
Note that this is only used to do the symbolic math needed to generate cell relationships. It is not used normally in GSAS-II.
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GSASIIlattice.
symInner
(M1, M2)[source]¶ Compute inner product of two square matrices with symbolic processing Use dot product because sympy does not define an inner product primitive
This requires that M1 & M2 be two sympy objects, as created in GenerateCellConstraints().
Note that this is only used to do the symbolic math needed to generate cell relationships. It is not used normally in GSAS-II.
4.6. GSASIIspc: Space group module¶
Space group interpretation routines. Note that space group information is stored in a Space Group (SGData) object.
-
GSASIIspc.
AllOps
(SGData)[source]¶ Returns a list of all operators for a space group, including those for centering and a center of symmetry
Parameters: SGData – from SpcGroup()
Returns: (SGTextList,offsetList,symOpList,G2oprList) where - SGTextList: a list of strings with formatted and normalized symmetry operators.
- offsetList: a tuple of (dx,dy,dz) offsets that relate the GSAS-II symmetry operation to the operator in SGTextList and symOpList. these dx (etc.) values are added to the GSAS-II generated positions to provide the positions that are generated by the normalized symmetry operators.
- symOpList: a list of tuples with the normalized symmetry
operations as (M,T) values
(see
SGOps
in the Space Group object) - G2oprList: a list with the GSAS-II operations for each symmetry operation as
a tuple with (center,mult,opnum,opcode), where center is (0,0,0), (0.5,0,0),
(0.5,0.5,0.5),…; where mult is 1 or -1 for the center of symmetry
where opnum is the number for the symmetry operation, in
SGOps
(starting with 0) and opcode is mult*(100*icen+j+1). - G2opcodes: a list with the name that GSAS-II uses for each symmetry operation (same as opcode, above)
-
GSASIIspc.
ApplyStringOpsMom
(A, SGData, SSGData, Mom)[source]¶ Applies string operations to modulated magnetic moment components used in drawing Drawing matches Bilbao MVISUALIZE
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GSASIIspc.
AtomDxSymFix
(Dx, SytSym, CSIX)[source]¶ Applies site symmetry restrictions to atom position shifts. 1st parameter value of each kind encountered is assumed to be the independent one. Needed for ISODISTORT mode shifts.
-
GSASIIspc.
ElemPosition
(SGData)[source]¶ Under development. Object here is to return a list of symmetry element types and locations suitable for say drawing them. So far I have the element type… getting all possible locations without lookup may be impossible!
-
GSASIIspc.
GenAtom
(XYZ, SGData, All=False, Uij=[], Move=True)[source]¶ Generates the equivalent positions for a specified coordinate and space group
Parameters: - XYZ – an array, tuple or list containing 3 elements: x, y & z
- SGData – from
SpcGroup()
- All – True return all equivalent positions including duplicates; False return only unique positions
- Uij – [U11,U22,U33,U12,U13,U23] or [] if no Uij
- Move – True move generated atom positions to be inside cell False do not move atoms
Returns: [[XYZEquiv],Idup,[UijEquiv],spnflp]
- [XYZEquiv] is list of equivalent positions (XYZ is first entry)
- Idup = [-][C]SS where SS is the symmetry operator number (1-24), C (if not 0,0,0)
- is centering operator number (1-4) and - is for inversion Cell = unit cell translations needed to put new positions inside cell [UijEquiv] - equivalent Uij; absent if no Uij given
- +1/-1 for spin inversion of operator - empty if not magnetic
-
GSASIIspc.
GenHKL
(HKL, SGData)[source]¶ Generates all equivlent reflections including Friedel pairs :param HKL: [h,k,l] must be integral values :param SGData: space group data obtained from SpcGroup :returns: array Uniq: equivalent reflections
-
GSASIIspc.
GenHKLf
(HKL, SGData)[source]¶ Uses old GSAS Fortran routine genhkl.for
Parameters: - HKL – [h,k,l] must be integral values for genhkl.for to work
- SGData – space group data obtained from SpcGroup
Returns: iabsnt,mulp,Uniq,phi
- iabsnt = True if reflection is forbidden by symmetry
- mulp = reflection multiplicity including Friedel pairs
- Uniq = numpy array of equivalent hkl in descending order of h,k,l
- phi = phase offset for each equivalent h,k,l
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GSASIIspc.
GetCSuinel
(siteSym)[source]¶ returns Uij terms, multipliers, GUI flags & Uiso2Uij multipliers
-
GSASIIspc.
GetGenSym
(SGData)[source]¶ Get the space group generator symbols :param SGData: from
SpcGroup()
LaueSym = (‘-1’,’2/m’,’mmm’,’4/m’,’4/mmm’,’3R’,’3mR’,’3’,’3m1’,’31m’,’6/m’,’6/mmm’,’m3’,’m3m’) LattSym = (‘P’,’A’,’B’,’C’,’I’,’F’,’R’)
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GSASIIspc.
GetLittleGrpOps
(SGData, vec)[source]¶ Find rotation part of operators that leave vec unchanged
Parameters: - SGData – space group data structure as defined in SpcGroup above.
- vec – a numpy array of fractional vector coordinates
Returns: Little - list of operators [M,T] that form the little gropu
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GSASIIspc.
GetNXUPQsym
(siteSym)[source]¶ The codes XUPQ are for lookup of symmetry constraints for position(X), thermal parm(U) & magnetic moments (P & Q)
-
GSASIIspc.
Latt2text
(Cen)[source]¶ From lattice centering vectors returns ‘;’ delimited cell centering vectors
-
GSASIIspc.
MT2text
(Opr, reverse=False)[source]¶ From space group matrix/translation operator returns text version
-
GSASIIspc.
MagSSText2MTS
(Opr, G2=False)[source]¶ From magnetic super space group cif text returns matrix/translation + spin flip
-
GSASIIspc.
MagSytSym
(SytSym, dupDir, SGData)[source]¶ site sym operations: 1,-1,2,3,-3,4,-4,6,-6,m need to be marked if spin inversion
-
GSASIIspc.
MagText2MTS
(mcifOpr, CIF=True)[source]¶ From magnetic space group cif text returns matrix/translation + spin flip
-
GSASIIspc.
MoveToUnitCell
(xyz)[source]¶ Translates a set of coordinates so that all values are >=0 and < 1
Parameters: xyz – a list or numpy array of fractional coordinates Returns: XYZ - numpy array of new coordinates now 0 or greater and less than 1
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GSASIIspc.
Muiso2Shkl
(muiso, SGData, cell)[source]¶ this is to convert isotropic mustrain to generalized Shkls
-
GSASIIspc.
Opposite
(XYZ, toler=0.0002)[source]¶ - Gives opposite corner, edge or face of unit cell for position within tolerance.
- Result may be just outside the cell within tolerance
Parameters: - XYZ – 0 >= np.array[x,y,z] > 1 as by MoveToUnitCell
- toler – unit cell fraction tolerance making opposite
Returns: XYZ: dict of opposite positions; key=unit cell & always contains XYZ
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GSASIIspc.
SGErrors
(IErr)[source]¶ Interprets the error message code from SpcGroup. Used in SpaceGroup.
Parameters: IErr – see SGError in SpcGroup()
Returns: ErrString - a string with the error message or “Unknown error”
-
GSASIIspc.
SGPrint
(SGData, AddInv=False)[source]¶ Print the output of SpcGroup in a nicely formatted way. Used in SpaceGroup
Parameters: SGData – from SpcGroup()
Returns: SGText - list of strings with the space group details SGTable - list of strings for each of the operations
-
GSASIIspc.
SGProd
(OpA, OpB)[source]¶ - Form space group operator product. OpA & OpB are [M,V] pairs;
- both must be of same dimension (3 or 4). Returns [M,V] pair
-
GSASIIspc.
SGPtGroup
(SGData)[source]¶ Determine point group of the space group - done after space group symbol has been evaluated by SpcGroup. Only short symbols are allowed
Parameters: SGData – from :func SpcGroup Returns: SSGPtGrp & SSGKl (only defaults for Mono & Ortho)
-
GSASIIspc.
SSChoice
(SGData)[source]¶ Gets the unique set of possible super space groups for a given space group
-
GSASIIspc.
SSGModCheck
(Vec, modSymb, newMod=True)[source]¶ Checks modulation vector compatibility with supersymmetry space group symbol. if newMod: Superspace group symbol takes precidence & the vector will be modified accordingly
-
GSASIIspc.
SSGPrint
(SGData, SSGData, AddInv=False)[source]¶ Print the output of SSpcGroup in a nicely formatted way. Used in SSpaceGroup
Parameters: - SGData – space group data structure as defined in SpcGroup above.
- SSGData – from
SSpcGroup()
Returns: SSGText - list of strings with the superspace group details SGTable - list of strings for each of the operations
-
GSASIIspc.
SSMT2text
(Opr)[source]¶ From superspace group matrix/translation operator returns text version
-
GSASIIspc.
SSpaceGroup
(SGSymbol, SSymbol)[source]¶ Print the output of SSpcGroup in a nicely formatted way.
Parameters: - SGSymbol – space group symbol with spaces between axial fields.
- SSymbol – superspace group symbol extension (string).
Returns: nothing
-
GSASIIspc.
SSpcGroup
(SGData, SSymbol)[source]¶ Determines supersymmetry information from superspace group name; currently only for (3+1) superlattices
Parameters: - SGData – space group data structure as defined in SpcGroup above (see SGData).
- SSymbol – superspace group symbol extension (string) defining modulation direction & generator info.
Returns: (SSGError,SSGData)
SGError = 0 for no errors; >0 for errors (see SGErrors below for details)
SSGData - is a dict (see Superspace Group object) with entries:
- ’SSpGrp’: full superspace group symbol, accidental spaces removed; for display only
- ’SSGCen’: 4D cell centering vectors [0,0,0,0] at least
- ’SSGOps’: 4D symmetry operations as [M,T] so that M*x+T = x’
-
GSASIIspc.
SpaceGroup
(SGSymbol)[source]¶ Print the output of SpcGroup in a nicely formatted way.
Parameters: SGSymbol – space group symbol (string) with spaces between axial fields Returns: nothing
-
GSASIIspc.
SpcGroup
(SGSymbol)[source]¶ Determines cell and symmetry information from a short H-M space group name
Parameters: SGSymbol – space group symbol (string) with spaces between axial fields Returns: (SGError,SGData) - SGError = 0 for no errors; >0 for errors (see SGErrors below for details)
- SGData - is a dict (see Space Group object) with entries:
- ’SpGrp’: space group symbol, slightly cleaned up
- ’SGFixed’: True if space group data can not be changed, e.g. from magnetic cif; otherwise False
- ’SGGray’: True if 1’ in symbol - gray group for mag. incommensurate phases
- ’SGLaue’: one of ‘-1’, ‘2/m’, ‘mmm’, ‘4/m’, ‘4/mmm’, ‘3R’, ‘3mR’, ‘3’, ‘3m1’, ‘31m’, ‘6/m’, ‘6/mmm’, ‘m3’, ‘m3m’
- ’SGInv’: boolean; True if centrosymmetric, False if not
- ’SGLatt’: one of ‘P’, ‘A’, ‘B’, ‘C’, ‘I’, ‘F’, ‘R’
- ’SGUniq’: one of ‘a’, ‘b’, ‘c’ if monoclinic, ‘’ otherwise
- ’SGCen’: cell centering vectors [0,0,0] at least
- ’SGOps’: symmetry operations as [M,T] so that M*x+T = x’
- ’SGSys’: one of ‘triclinic’, ‘monoclinic’, ‘orthorhombic’, ‘tetragonal’, ‘rhombohedral’, ‘trigonal’, ‘hexagonal’, ‘cubic’
- ’SGPolax’: one of ‘ ‘, ‘x’, ‘y’, ‘x y’, ‘z’, ‘x z’, ‘y z’, ‘xyz’, ‘111’ for arbitrary axes
- ’SGPtGrp’: one of 32 point group symbols (with some permutations), which
- is filled by SGPtGroup, is external (KE) part of supersymmetry point group
- ’SSGKl’: default internal (Kl) part of supersymmetry point group; modified
- in supersymmetry stuff depending on chosen modulation vector for Mono & Ortho
- ’BNSlattsym’: BNS lattice symbol & cenering op - used for magnetic structures
-
GSASIIspc.
StandardizeSpcName
(spcgroup)[source]¶ Accept a spacegroup name where spaces may have not been used in the names according to the GSAS convention (spaces between symmetry for each axis) and return the space group name as used in GSAS
-
GSASIIspc.
StringOpsProd
(A, B, SGData)[source]¶ Find A*B where A & B are in strings ‘-’ + ‘100*c+n’ + ‘+ijk’ where ‘-’ indicates inversion, c(>0) is the cell centering operator, n is operator number from SgOps and ijk are unit cell translations (each may be <0). Should return resultant string - C. SGData - dictionary using entries:
- ‘SGCen’: cell centering vectors [0,0,0] at least
- ‘SGOps’: symmetry operations as [M,T] so that M*x+T = x’
-
GSASIIspc.
SytSym
(XYZ, SGData)[source]¶ Generates the number of equivalent positions and a site symmetry code for a specified coordinate and space group
Parameters: - XYZ – an array, tuple or list containing 3 elements: x, y & z
- SGData – from SpcGroup
Returns: a four element tuple:
- The 1st element is a code for the site symmetry (see GetKNsym)
- The 2nd element is the site multiplicity
- Ndup number of overlapping operators
- dupDir Dict - dictionary of overlapping operators
-
GSASIIspc.
TextOps
(text, table, reverse=False)[source]¶ Makes formatted operator list :param text,table: arrays of text made by SGPrint :param reverse: True for x+1/2 form; False for 1/2+x form :returns: OpText: full list of symmetry operators; one operation per line generally printed to console for use via cut/paste in other programs, but could be used for direct input
-
GSASIIspc.
UpdateSytSym
(Phase)[source]¶ Update site symmetry/site multiplicity after space group/BNS lattice change
-
GSASIIspc.
altSettingOrtho
= {'A b a 2': {'abc': 'A b a 2', 'acb': 'A c 2 a', 'bac': 'B b a 2', 'bca': 'C c 2 a', 'cab': 'B 2 c b', 'cba': 'C 2 c b'}, 'A b m 2': {'abc': 'A b m 2', 'acb': 'A c 2 m', 'bac': 'B m a 2', 'bca': 'C m 2 a', 'cab': 'B 2 c m', 'cba': 'C 2 m b'}, 'A m a 2': {'abc': 'A m a 2', 'acb': 'A m 2 a', 'bac': 'B b m 2', 'bca': 'C c 2 m', 'cab': 'B 2 m b', 'cba': 'C 2 c m'}, 'A m m 2': {'abc': 'A m m 2', 'acb': 'A m 2 m', 'bac': 'B m m 2', 'bca': 'C m 2 m', 'cab': 'B 2 m m', 'cba': 'C 2 m m'}, 'C 2 2 2': {'abc': 'C 2 2 2', 'acb': 'B 2 2 2', 'bac': 'C 2 2 2', 'bca': 'B 2 2 2', 'cab': 'A 2 2 2', 'cba': 'A 2 2 2'}, 'C 2 2 21': {'abc': 'C 2 2 21', 'acb': 'B 2 21 2', 'bac': 'C 2 2 21', 'bca': 'B 2 21 2', 'cab': 'A 21 2 2', 'cba': 'A 21 2 2'}, 'C c c 2': {'abc': 'C c c 2', 'acb': 'B b 2 b', 'bac': 'C c c 2', 'bca': 'B b 2 b', 'cab': 'A 2 a a', 'cba': 'A 2 a a'}, 'C c c a': {'abc': 'C c a a', 'acb': 'B b a b', 'bac': 'C c c b', 'bca': 'B b c b', 'cab': 'A b a a', 'cba': 'A c a a'}, 'C c c m': {'abc': 'C c c m', 'acb': 'B b m b', 'bac': 'C c c m', 'bca': 'B b m b', 'cab': 'A m a a', 'cba': 'A m a a'}, 'C m c 21': {'abc': 'C m c 21', 'acb': 'B m 21 b', 'bac': 'C c m 21', 'bca': 'B b 21 m', 'cab': 'A 21 m a', 'cba': 'A 21 a m'}, 'C m c a': {'abc': 'C m c a', 'acb': 'B m a b', 'bac': 'C c m b', 'bca': 'B b c m', 'cab': 'A b m a', 'cba': 'A c a m'}, 'C m c m': {'abc': 'C m c m', 'acb': 'B m m b', 'bac': 'C c m m', 'bca': 'B b m m', 'cab': 'A m m a', 'cba': 'A m a m'}, 'C m m 2': {'abc': 'C m m 2', 'acb': 'B m 2 m', 'bac': 'C m m 2', 'bca': 'B m 2 m', 'cab': 'A 2 m m', 'cba': 'A 2 m m'}, 'C m m a': {'abc': 'C m m a', 'acb': 'B m a m', 'bac': 'C m m b', 'bca': 'B m c m', 'cab': 'A b m m', 'cba': 'A c m m'}, 'C m m m': {'abc': 'C m m m', 'acb': 'B m m m', 'bac': 'C m m m', 'bca': 'B m m m', 'cab': 'A m m m', 'cba': 'A m m m'}, 'F 2 2 2': {'abc': 'F 2 2 2', 'acb': 'F 2 2 2', 'bac': 'F 2 2 2', 'bca': 'F 2 2 2', 'cab': 'F 2 2 2', 'cba': 'F 2 2 2'}, 'F d d 2': {'abc': 'F d d 2', 'acb': 'F d 2 d', 'bac': 'F d d 2', 'bca': 'F d 2 d', 'cab': 'F 2 d d', 'cba': 'F 2 d d'}, 'F d d d': {'abc': 'F d d d', 'acb': 'F d d d', 'bac': 'F d d d', 'bca': 'F d d d', 'cab': 'F d d d', 'cba': 'F d d d'}, 'F m m 2': {'abc': 'F m m 2', 'acb': 'F m 2 m', 'bac': 'F m m 2', 'bca': 'F m 2 m', 'cab': 'F 2 m m', 'cba': 'F 2 m m'}, 'F m m m': {'abc': 'F m m m', 'acb': 'F m m m', 'bac': 'F m m m', 'bca': 'F m m m', 'cab': 'F m m m', 'cba': 'F m m m'}, 'I 2 2 2': {'abc': 'I 2 2 2', 'acb': 'I 2 2 2', 'bac': 'I 2 2 2', 'bca': 'I 2 2 2', 'cab': 'I 2 2 2', 'cba': 'I 2 2 2'}, 'I 21 21 21': {'abc': 'I 21 21 21', 'acb': 'I 21 21 21', 'bac': 'I 21 21 21', 'bca': 'I 21 21 21', 'cab': 'I 21 21 21', 'cba': 'I 21 21 21'}, 'I b a 2': {'abc': 'I b a 2', 'acb': 'I c 2 a', 'bac': 'I b a 2', 'bca': 'I c 2 a', 'cab': 'I 2 c b', 'cba': 'I 2 c b'}, 'I b a m': {'abc': 'I b a m', 'acb': 'I c m a', 'bac': 'I b a m', 'bca': 'I c m a', 'cab': 'I m c b', 'cba': 'I m c b'}, 'I b c a': {'abc': 'I b c a', 'acb': 'I c a b', 'bac': 'I c a b', 'bca': 'I b c a', 'cab': 'I b c a', 'cba': 'I c a b'}, 'I m a 2': {'abc': 'I m a 2', 'acb': 'I m 2 a', 'bac': 'I b m 2', 'bca': 'I c 2 m', 'cab': 'I 2 m b', 'cba': 'I 2 c m'}, 'I m m 2': {'abc': 'I m m 2', 'acb': 'I m 2 m', 'bac': 'I m m 2', 'bca': 'I m 2 m', 'cab': 'I 2 m m', 'cba': 'I 2 m m'}, 'I m m a': {'abc': 'I m m a', 'acb': 'I m a m', 'bac': 'I m m b', 'bca': 'I m c m', 'cab': 'I b m m', 'cba': 'I c m m'}, 'I m m m': {'abc': 'I m m m', 'acb': 'I m m m', 'bac': 'I m m m', 'bca': 'I m m m', 'cab': 'I m m m', 'cba': 'I m m m'}, 'P 2 2 2': {'abc': 'P 2 2 2', 'acb': 'P 2 2 2', 'bac': 'P 2 2 2', 'bca': 'P 2 2 2', 'cab': 'P 2 2 2', 'cba': 'P 2 2 2'}, 'P 2 2 21': {'abc': 'P 2 2 21', 'acb': 'P 2 21 2', 'bac': 'P 2 2 21', 'bca': 'P 2 21 2', 'cab': 'P 21 2 2', 'cba': 'P 21 2 2'}, 'P 21 21 2': {'abc': 'P 21 21 2', 'acb': 'P 21 2 21', 'bac': 'P 21 21 2', 'bca': 'P 21 2 21', 'cab': 'P 2 21 21', 'cba': 'P 2 21 21'}, 'P 21 21 21': {'abc': 'P 21 21 21', 'acb': 'P 21 21 21', 'bac': 'P 21 21 21', 'bca': 'P 21 21 21', 'cab': 'P 21 21 21', 'cba': 'P 21 21 21'}, 'P b a 2': {'abc': 'P b a 2', 'acb': 'P c 2 a', 'bac': 'P b a 2', 'bca': 'P c 2 a', 'cab': 'P 2 c b', 'cba': 'P 2 c b'}, 'P b a m': {'abc': 'P b a m', 'acb': 'P c m a', 'bac': 'P b a m', 'bca': 'P c m a', 'cab': 'P m c b', 'cba': 'P m c b'}, 'P b a n': {'abc': 'P b a n', 'acb': 'P c n a', 'bac': 'P b a n', 'bca': 'P c n a', 'cab': 'P n c b', 'cba': 'P n c b'}, 'P b c a': {'abc': 'P b c a', 'acb': 'P c a b', 'bac': 'P c a b', 'bca': 'P b c a', 'cab': 'P b c a', 'cba': 'P c a b'}, 'P b c m': {'abc': 'P b c m', 'acb': 'P c m b', 'bac': 'P c a m', 'bca': 'P b m a', 'cab': 'P m c a', 'cba': 'P m a b'}, 'P b c n': {'abc': 'P b c n', 'acb': 'P c n b', 'bac': 'P c a n', 'bca': 'P b n a', 'cab': 'P n c a', 'cba': 'P n a b'}, 'P c a 21': {'abc': 'P c a 21', 'acb': 'P b 21 a', 'bac': 'P b c 21', 'bca': 'P c 21 b', 'cab': 'P 21 a b', 'cba': 'P 21 c a'}, 'P c c 2': {'abc': 'P c c 2', 'acb': 'P b 2 b', 'bac': 'P c c 2', 'bca': 'P b 2 b', 'cab': 'P 2 a a', 'cba': 'P 2 a a'}, 'P c c a': {'abc': 'P c c a', 'acb': 'P b a b', 'bac': 'P c c b', 'bca': 'P b c b', 'cab': 'P b a a', 'cba': 'P c a a'}, 'P c c m': {'abc': 'P c c m', 'acb': 'P b m b', 'bac': 'P c c m', 'bca': 'P b m b', 'cab': 'P m a a', 'cba': 'P m a a'}, 'P c c n': {'abc': 'P c c n', 'acb': 'P b n b', 'bac': 'P c c n', 'bca': 'P b n b', 'cab': 'P n a a', 'cba': 'P n a a'}, 'P m a 2': {'abc': 'P m a 2', 'acb': 'P m 2 a', 'bac': 'P b m 2', 'bca': 'P c 2 m', 'cab': 'P 2 m b', 'cba': 'P 2 c m'}, 'P m c 21': {'abc': 'P m c 21', 'acb': 'P m 21 b', 'bac': 'P c m 21', 'bca': 'P b 21 m', 'cab': 'P 21 m a', 'cba': 'P 21 a m'}, 'P m m 2': {'abc': 'P m m 2', 'acb': 'P m 2 m', 'bac': 'P m m 2', 'bca': 'P m 2 m', 'cab': 'P 2 m m', 'cba': 'P 2 m m'}, 'P m m a': {'abc': 'P m m a', 'acb': 'P m a m', 'bac': 'P m m b', 'bca': 'P m c m', 'cab': 'P b m m', 'cba': 'P c m m'}, 'P m m m': {'abc': 'P m m m', 'acb': 'P m m m', 'bac': 'P m m m', 'bca': 'P m m m', 'cab': 'P m m m', 'cba': 'P m m m'}, 'P m m n': {'abc': 'P m m n', 'acb': 'P m n m', 'bac': 'P m m n', 'bca': 'P m n m', 'cab': 'P n m m', 'cba': 'P n m m'}, 'P m n 21': {'abc': 'P m n 21', 'acb': 'P m 21 n', 'bac': 'P n m 21', 'bca': 'P n 21 m', 'cab': 'P 21 m n', 'cba': 'P 21 n m'}, 'P m n a': {'abc': 'P m n a', 'acb': 'P m a n', 'bac': 'P n m b', 'bca': 'P n c m', 'cab': 'P b m n', 'cba': 'P c n m'}, 'P n a 21': {'abc': 'P n a 21', 'acb': 'P n 21 a', 'bac': 'P b n 21', 'bca': 'P c 21 n', 'cab': 'P 21 n b', 'cba': 'P 21 c n'}, 'P n c 2': {'abc': 'P n c 2', 'acb': 'P n 2 b', 'bac': 'P c n 2', 'bca': 'P b 2 n', 'cab': 'P 2 n a', 'cba': 'P 2 a n'}, 'P n m a': {'abc': 'P n m a', 'acb': 'P n a m', 'bac': 'P m n b', 'bca': 'P m c n', 'cab': 'P b n m', 'cba': 'P c m n'}, 'P n n 2': {'abc': 'P n n 2', 'acb': 'P n 2 n', 'bac': 'P n n 2', 'bca': 'P n 2 n', 'cab': 'P 2 n n', 'cba': 'P 2 n n'}, 'P n n a': {'abc': 'P n n a', 'acb': 'P n a n', 'bac': 'P n n b', 'bca': 'P n c n', 'cab': 'P b n n', 'cba': 'P c n n'}, 'P n n m': {'abc': 'P n n m', 'acb': 'P n m n', 'bac': 'P n n m', 'bca': 'P n m n', 'cab': 'P m n n', 'cba': 'P m n n'}, 'P n n n': {'abc': 'P n n n', 'acb': 'P n n n', 'bac': 'P n n n', 'bca': 'P n n n', 'cab': 'P n n n', 'cba': 'P n n n'}}¶ A dictionary of alternate settings for orthorhombic unit cells
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GSASIIspc.
checkHKLextc
(HKL, SGData)[source]¶ Checks if reflection extinct - does not check centering
Parameters: - HKL – [h,k,l]
- SGData – space group data obtained from SpcGroup
Returns: True if extinct; False if allowed
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GSASIIspc.
checkMagextc
(HKL, SGData)[source]¶ Checks if reflection magnetically extinct; does fullcheck (centering, too) uses algorthm from Gallego, et al., J. Appl. Cryst. 45, 1236-1247 (2012)
Parameters: - HKL – [h,k,l]
- SGData – space group data obtained from SpcGroup; must have magnetic symmetry SpnFlp data
Returns: True if magnetically extinct; False if allowed (to match GenHKLf)
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GSASIIspc.
fullHM2shortHM
(SpcGp)[source]¶ Accepts a full H-M space group symbol and returns a short H-M symbol that the space group interpreter can translate
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GSASIIspc.
selftestlist
= [<function test0>, <function test1>, <function test2>, <function test3>]¶ Defines a list of self-tests
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GSASIIspc.
sgequiv_2002_orthorhombic
= {'AE2A': 'A c 2 a', 'AE2M': 'A c 2 m', 'AEA2': 'A b a 2', 'AEAA': 'A b a a', 'AEAM': 'A c a m', 'AEM2': 'A b m 2', 'AEMA': 'A b m a', 'AEMM': 'A b m m', 'B2EB': 'B 2 c b', 'B2EM': 'B 2 c m', 'BBE2': 'B b a 2', 'BBEB': 'B b c b', 'BBEM': 'B b c m', 'BME2': 'B m a 2', 'BMEB': 'B m a b', 'BMEM': 'B m c m', 'C2CE': 'C 2 c b', 'C2ME': 'C 2 m b', 'CC2E': 'C c 2 a', 'CCCE': 'C c c a', 'CCME': 'C c m b', 'CM2E': 'C m 2 a', 'CMCE': 'C m c a', 'CMME': 'C m m a'}¶ A dictionary of orthorhombic space groups that were renamed in the 2002 Volume A, along with the pre-2002 name. The e designates a double glide-plane
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GSASIIspc.
spg2origins
= {'A b a a': [-0.25, 0, -0.25], 'A c a a': [-0.25, -0.25, 0], 'B b a b': [0, -0.25, -0.25], 'B b c b': [-0.25, -0.25, 0], 'C c c a': [0, -0.25, -0.25], 'C c c b': [-0.25, 0, -0.25], 'F d - c': [-0.375, -0.375, -0.375], 'F d -3': [-0.125, -0.125, -0.125], 'F d -3 c': [-0.375, -0.375, -0.375], 'F d -3 m': [-0.125, -0.125, -0.125], 'F d 3': [-0.125, -0.125, -0.125], 'F d 3 m': [-0.125, -0.125, -0.125], 'F d d d': [-0.125, -0.125, -0.125], 'I 41/a': [0, -0.25, -0.125], 'I 41/a c d': [0, 0.25, -0.125], 'I 41/a m d': [0, 0.25, -0.125], 'P 4/n': [-0.25, -0.25, 0], 'P 4/n b m': [-0.25, -0.25, 0], 'P 4/n c c': [-0.25, -0.25, 0], 'P 4/n m m': [-0.25, -0.25, 0], 'P 4/n n c': [-0.25, -0.25, -0.25], 'P 42/n': [-0.25, -0.25, -0.25], 'P 42/n b c': [-0.25, -0.25, -0.25], 'P 42/n c m': [-0.25, 0.25, -0.25], 'P 42/n m c': [-0.25, 0.25, -0.25], 'P 42/n n m': [-0.25, 0.25, -0.25], 'P b a n': [-0.25, -0.25, 0], 'P c n a': [-0.25, 0, -0.25], 'P m m n': [-0.25, -0.25, 0], 'P m n m': [-0.25, 0, -0.25], 'P n -3 m': [-0.25, -0.25, -0.25], 'P n -3 n': [-0.25, -0.25, -0.25], 'P n 3 m': [-0.25, -0.25, -0.25], 'P n 3 n': [-0.25, -0.25, -0.25], 'P n c b': [0, -0.25, -0.25], 'P n m m': [0, -0.25, -0.25], 'P n n n': [-0.25, -0.25, -0.25], 'p n -3': [-0.25, -0.25, -0.25], 'p n 3': [-0.25, -0.25, -0.25]}¶ A dictionary of all spacegroups that have 2nd settings; the value is the 1st –> 2nd setting transformation vector as X(2nd) = X(1st)-V, nonstandard ones are included.
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GSASIIspc.
spgbyNum
= [None, 'P 1', 'P -1', 'P 2', 'P 21', 'C 2', 'P m', 'P c', 'C m', 'C c', 'P 2/m', 'P 21/m', 'C 2/m', 'P 2/c', 'P 21/c', 'C 2/c', 'P 2 2 2', 'P 2 2 21', 'P 21 21 2', 'P 21 21 21', 'C 2 2 21', 'C 2 2 2', 'F 2 2 2', 'I 2 2 2', 'I 21 21 21', 'P m m 2', 'P m c 21', 'P c c 2', 'P m a 2', 'P c a 21', 'P n c 2', 'P m n 21', 'P b a 2', 'P n a 21', 'P n n 2', 'C m m 2', 'C m c 21', 'C c c 2', 'A m m 2', 'A b m 2', 'A m a 2', 'A b a 2', 'F m m 2', 'F d d 2', 'I m m 2', 'I b a 2', 'I m a 2', 'P m m m', 'P n n n', 'P c c m', 'P b a n', 'P m m a', 'P n n a', 'P m n a', 'P c c a', 'P b a m', 'P c c n', 'P b c m', 'P n n m', 'P m m n', 'P b c n', 'P b c a', 'P n m a', 'C m c m', 'C m c a', 'C m m m', 'C c c m', 'C m m a', 'C c c a', 'F m m m', 'F d d d', 'I m m m', 'I b a m', 'I b c a', 'I m m a', 'P 4', 'P 41', 'P 42', 'P 43', 'I 4', 'I 41', 'P -4', 'I -4', 'P 4/m', 'P 42/m', 'P 4/n', 'P 42/n', 'I 4/m', 'I 41/a', 'P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2', 'I 4 2 2', 'I 41 2 2', 'P 4 m m', 'P 4 b m', 'P 42 c m', 'P 42 n m', 'P 4 c c', 'P 4 n c', 'P 42 m c', 'P 42 b c', 'I 4 m m', 'I 4 c m', 'I 41 m d', 'I 41 c d', 'P -4 2 m', 'P -4 2 c', 'P -4 21 m', 'P -4 21 c', 'P -4 m 2', 'P -4 c 2', 'P -4 b 2', 'P -4 n 2', 'I -4 m 2', 'I -4 c 2', 'I -4 2 m', 'I -4 2 d', 'P 4/m m m', 'P 4/m c c', 'P 4/n b m', 'P 4/n n c', 'P 4/m b m', 'P 4/m n c', 'P 4/n m m', 'P 4/n c c', 'P 42/m m c', 'P 42/m c m', 'P 42/n b c', 'P 42/n n m', 'P 42/m b c', 'P 42/m n m', 'P 42/n m c', 'P 42/n c m', 'I 4/m m m', 'I 4/m c m', 'I 41/a m d', 'I 41/a c d', 'P 3', 'P 31', 'P 32', 'R 3', 'P -3', 'R -3', 'P 3 1 2', 'P 3 2 1', 'P 31 1 2', 'P 31 2 1', 'P 32 1 2', 'P 32 2 1', 'R 3 2', 'P 3 m 1', 'P 3 1 m', 'P 3 c 1', 'P 3 1 c', 'R 3 m', 'R 3 c', 'P -3 1 m', 'P -3 1 c', 'P -3 m 1', 'P -3 c 1', 'R -3 m', 'R -3 c', 'P 6', 'P 61', 'P 65', 'P 62', 'P 64', 'P 63', 'P -6', 'P 6/m', 'P 63/m', 'P 6 2 2', 'P 61 2 2', 'P 65 2 2', 'P 62 2 2', 'P 64 2 2', 'P 63 2 2', 'P 6 m m', 'P 6 c c', 'P 63 c m', 'P 63 m c', 'P -6 m 2', 'P -6 c 2', 'P -6 2 m', 'P -6 2 c', 'P 6/m m m', 'P 6/m c c', 'P 63/m c m', 'P 63/m m c', 'P 2 3', 'F 2 3', 'I 2 3', 'P 21 3', 'I 21 3', 'P m 3', 'P n 3', 'F m -3', 'F d -3', 'I m -3', 'P a -3', 'I a -3', 'P 4 3 2', 'P 42 3 2', 'F 4 3 2', 'F 41 3 2', 'I 4 3 2', 'P 43 3 2', 'P 41 3 2', 'I 41 3 2', 'P -4 3 m', 'F -4 3 m', 'I -4 3 m', 'P -4 3 n', 'F -4 3 c', 'I -4 3 d', 'P m -3 m', 'P n -3 n', 'P m -3 n', 'P n -3 m', 'F m -3 m', 'F m -3 c', 'F d -3 m', 'F d -3 c', 'I m -3 m', 'I a -3 d']¶ Space groups indexed by number
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GSASIIspc.
spglist
= {'A2/m': ('A 2', 'A m', 'A a', 'A n', 'A 2/m', 'A 2/a', 'A 2/n'), 'Ammm': ('A 21 2 2', 'A 2 2 2', 'A 2 m m', 'A 21 m a', 'A 21 a m', 'A 2 a a', 'A m 2 m', 'A m m 2', 'A b m 2', 'A c 2 m', 'A m a 2', 'A m 2 a', 'A b a 2', 'A c 2 a', 'A m m a', 'A m a m', 'A b m a', 'A c a m', 'A m m m', 'A m a a', 'A b m m', 'A c m m', 'A c a a', 'A b a a'), 'Bmmm': ('B 2 21 2', 'B 2 2 2', 'B m 2 m', 'B m 21 b', 'B b 21 m', 'B b 2 b', 'B m m 2', 'B 2 m m', 'B 2 c m', 'B m a 2', 'B 2 m b', 'B b m 2', 'B 2 c b', 'B b a 2', 'B b m m', 'B m m b', 'B b c m', 'B m a b', 'B m m m', 'B b m b', 'B m a m', 'B m c m', 'B b a b', 'B b c b'), 'C1': ('C 1', 'C -1'), 'C2/m': ('C 2', 'C m', 'C c', 'C n', 'C 2/m', 'C 2/c', 'C 2/n'), 'Cmmm': ('C 2 2 21', 'C 2 2 2', 'C m m 2', 'C m c 21', 'C c m 21', 'C c c 2', 'C m 2 m', 'C 2 m m', 'C m 2 a', 'C 2 m b', 'C c 2 m', 'C 2 c m', 'C c 2 a', 'C 2 c b', 'C m c m', 'C c m m', 'C m c a', 'C c m b', 'C m m m', 'C c c m', 'C m m a', 'C m m b', 'C c c a', 'C c c b'), 'Fm3m': ('F 2 3', 'F m 3', 'F m -3', 'F d 3', 'F d -3', 'F 4 3 2', 'F 41 3 2', 'F -4 3 m', 'F -4 3 c', 'F m 3 m', 'F m -3 m', 'F m 3 c', 'F m -3 c', 'F d 3 m', 'F d -3 m', 'F d 3 c', 'F d -3 c'), 'Fmmm': ('F 2 2 2', 'F m m m', 'F d d d', 'F m m 2', 'F m 2 m', 'F 2 m m', 'F d d 2', 'F d 2 d', 'F 2 d d'), 'I2/m': ('I 2', 'I m', 'I a', 'I n', 'I c', 'I 2/m', 'I 2/a', 'I 2/c', 'I 2/n'), 'I4/mmm': ('I 4', 'I 41', 'I -4', 'I 4/m', 'I 41/a', 'I 4 2 2', 'I 41 2 2', 'I 4 m m', 'I 4 c m', 'I 41 m d', 'I 41 c d', 'I -4 m 2', 'I -4 c 2', 'I -4 2 m', 'I -4 2 d', 'I 4/m m m', 'I 4/m c m', 'I 41/a m d', 'I 41/a c d'), 'Im3m': ('I 2 3', 'I 21 3', 'I m 3', 'I m -3', 'I a 3', 'I a -3', 'I 4 3 2', 'I 41 3 2', 'I -4 3 m', 'I -4 3 d', 'I m -3 m', 'I m 3 m', 'I a 3 d', 'I a -3 d', 'I n 3 n', 'I n -3 n'), 'Immm': ('I 2 2 2', 'I 21 21 21', 'I m m 2', 'I m 2 m', 'I 2 m m', 'I b a 2', 'I 2 c b', 'I c 2 a', 'I m a 2', 'I 2 m b', 'I c 2 m', 'I m 2 a', 'I b m 2', 'I 2 c m', 'I m m m', 'I b a m', 'I m c b', 'I c m a', 'I b c a', 'I c a b', 'I m m a', 'I b m m ', 'I m c m', 'I m a m', 'I m m b', 'I c m m'), 'P1': ('P 1', 'P -1'), 'P2/m': ('P 2', 'P 21', 'P m', 'P a', 'P c', 'P n', 'P 2/m', 'P 21/m', 'P 2/c', 'P 2/a', 'P 2/n', 'P 21/c', 'P 21/a', 'P 21/n'), 'P4/mmm': ('P 4', 'P 41', 'P 42', 'P 43', 'P -4', 'P 4/m', 'P 42/m', 'P 4/n', 'P 42/n', 'P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2', 'P 4 m m', 'P 4 b m', 'P 42 c m', 'P 42 n m', 'P 4 c c', 'P 4 n c', 'P 42 m c', 'P 42 b c', 'P -4 2 m', 'P -4 2 c', 'P -4 21 m', 'P -4 21 c', 'P -4 m 2', 'P -4 c 2', 'P -4 b 2', 'P -4 n 2', 'P 4/m m m', 'P 4/m c c', 'P 4/n b m', 'P 4/n n c', 'P 4/m b m', 'P 4/m n c', 'P 4/n m m', 'P 4/n c c', 'P 42/m m c', 'P 42/m c m', 'P 42/n b c', 'P 42/n n m', 'P 42/m b c', 'P 42/m n m', 'P 42/n m c', 'P 42/n c m'), 'P6/mmm': ('P 3', 'P 31', 'P 32', 'P -3', 'P 3 1 2', 'P 3 2 1', 'P 31 1 2', 'P 31 2 1', 'P 32 1 2', 'P 32 2 1', 'P 3 m 1', 'P 3 1 m', 'P 3 c 1', 'P 3 1 c', 'P -3 1 m', 'P -3 1 c', 'P -3 m 1', 'P -3 c 1', 'P 6', 'P 61', 'P 65', 'P 62', 'P 64', 'P 63', 'P -6', 'P 6/m', 'P 63/m', 'P 6 2 2', 'P 61 2 2', 'P 65 2 2', 'P 62 2 2', 'P 64 2 2', 'P 63 2 2', 'P 6 m m', 'P 6 c c', 'P 63 c m', 'P 63 m c', 'P -6 m 2', 'P -6 c 2', 'P -6 2 m', 'P -6 2 c', 'P 6/m m m', 'P 6/m c c', 'P 63/m c m', 'P 63/m m c'), 'Pm3m': ('P 2 3', 'P 21 3', 'P m 3', 'P m -3', 'P n 3', 'P n -3', 'P a 3', 'P a -3', 'P 4 3 2', 'P 42 3 2', 'P 43 3 2', 'P 41 3 2', 'P -4 3 m', 'P -4 3 n', 'P m 3 m', 'P m -3 m', 'P n 3 n', 'P n -3 n', 'P m 3 n', 'P m -3 n', 'P n 3 m', 'P n -3 m'), 'Pmmm': ('P 2 2 2', 'P 2 2 21', 'P 21 2 2', 'P 2 21 2', 'P 21 21 2', 'P 2 21 21', 'P 21 2 21', 'P 21 21 21', 'P m m 2', 'P 2 m m', 'P m 2 m', 'P m c 21', 'P 21 m a', 'P b 21 m', 'P m 21 b', 'P c m 21', 'P 21 a m', 'P c c 2', 'P 2 a a', 'P b 2 b', 'P m a 2', 'P 2 m b', 'P c 2 m', 'P m 2 a', 'P b m 2', 'P 2 c m', 'P c a 21', 'P 21 a b', 'P c 21 b', 'P b 21 a', 'P b c 21', 'P 21 c a', 'P n c 2', 'P 2 n a', 'P b 2 n', 'P n 2 b', 'P c n 2', 'P 2 a n', 'P m n 21', 'P 21 m n', 'P n 21 m', 'P m 21 n', 'P n m 21', 'P 21 n m', 'P b a 2', 'P 2 c b', 'P c 2 a', 'P n a 21', 'P 21 n b', 'P c 21 n', 'P n 21 a', 'P b n 21', 'P 21 c n', 'P n n 2', 'P 2 n n', 'P n 2 n', 'P m m m', 'P n n n', 'P c c m', 'P m a a', 'P b m b', 'P b a n', 'P n c b', 'P c n a', 'P m m a', 'P b m m', 'P m c m', 'P m a m', 'P m m b', 'P c m m', 'P n n a', 'P b n n', 'P n c n', 'P n a n', 'P n n b', 'P c n n', 'P m n a', 'P b m n', 'P n c m', 'P m a n', 'P n m b', 'P c n m', 'P c c a', 'P b a a', 'P b c b', 'P b a b', 'P c c b', 'P c a a', 'P b a m', 'P m c b', 'P c m a', 'P c c n', 'P n a a', 'P b n b', 'P b c m', 'P m c a', 'P b m a', 'P c m b', 'P c a m', 'P m a b', 'P n n m', 'P m n n', 'P n m n', 'P m m n', 'P n m m', 'P m n m', 'P b c n', 'P n c a', 'P b n a', 'P c n b', 'P c a n', 'P n a b', 'P b c a', 'P c a b', 'P n m a', 'P b n m', 'P m c n', 'P n a m', 'P m n b', 'P c m n'), 'R3-H': ('R 3', 'R -3', 'R 3 2', 'R 3 m', 'R 3 c', 'R -3 m', 'R -3 c')}¶ A dictionary of space groups as ordered and named in the pre-2002 International Tables Volume A, except that spaces are used following the GSAS convention to separate the different crystallographic directions. Note that the symmetry codes here will recognize many non-standard space group symbols with different settings. They are ordered by Laue group
4.7. GSASIIdata: Data for computations¶
At present this module defines one dict, ramachandranDist
,
which contains arrays for All and specific amino acids.
4.8. GSASIIfiles: data (non-GUI) I/O routines¶
Module with miscellaneous routines for input and output from files.
This module should not contain any references to wxPython so that it can be imported for scriptable use or potentially on clients where wx is not installed.
Future refactoring: This module and GSASIIIO.py needs some work to move non-wx routines here. It may will likely make sense to rename the module(s) at that point.
-
GSASIIfiles.
G2Print
(*args, **kwargs)[source]¶ Print with filtering based level of output (see
G2SetPrintLevel()
). Use G2Print() as replacement for print().Parameters: mode (str) – if specified, this should contain the mode for printing (‘error’, ‘warn’ or anything else). If not specified, the first argument of the print command (args[0]) should contain the string ‘error’ for error messages and ‘warn’ for warning messages (capitalization and additional letters ignored.)
-
GSASIIfiles.
G2SetPrintLevel
(level)[source]¶ Set the level of output from calls to
G2Print()
, which should be used in place of print() within GSASII. Settings for the mode are ‘all’, ‘warn’, ‘error’ or ‘none’Parameters: level (str) – a string used to set the print level, which may be ‘all’, ‘warn’, ‘error’ or ‘none’. Note that capitalization and extra letters in level are ignored, so ‘Warn’, ‘warnings’, etc. will all set the mode to ‘warn’
-
GSASIIfiles.
G2printLevel
= 'all'¶ This defines the level of output from calls to
G2Print()
, which should be used in place of print() within this module. Settings for this are ‘all’, ‘warn’, ‘error’ or ‘none’. Also see:G2Print()
andG2SetPrintLevel()
.
-
GSASIIfiles.
GetColumnMetadata
(reader)[source]¶ Add metadata to an image from a column-type metadata file using
readColMetadata()
Parameters: reader – a reader object from reading an image
-
GSASIIfiles.
LoadImportRoutines
(prefix, errprefix=None, traceback=False)[source]¶ Routine to locate GSASII importers matching a prefix string
-
GSASIIfiles.
PDFWrite
(PDFentry, fileroot, PDFsaves, PDFControls, Inst={}, Limits=[])[source]¶ Write PDF-related data (G(r), S(Q),…) into files, as selected.
Parameters: - PDFentry (str) – name of the PDF entry in the tree. This is used for comments in the file specifying where it came from; it can be arbitrary
- fileroot (str) – name of file(s) to be written. The extension will be ignored.
- PDFsaves (list) – flags that determine what type of file will be written: PDFsaves[0], if True writes a I(Q) file with a .iq extension PDFsaves[1], if True writes a S(Q) file with a .sq extension PDFsaves[2], if True writes a F(Q) file with a .fq extension PDFsaves[3], if True writes a G(r) file with a .gr extension PDFsaves[4], if True writes G(r) in a pdfGUI input file with a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are both True, the pdfGUI overwrites the G(r) file. PDFsaves[5], if True writes F(Q) & g(R) with .fq & .gr extensions overwrites these if selected by option 2, 3 or 4
- PDFControls (dict) – The PDF parameters and computed results
- Inst (dict) – Instrument parameters from the PDWR entry used to compute the PDF. Needed only when PDFsaves[4] is True.
- Limits (list) – Computation limits from the PDWR entry used to compute the PDF. Needed only when PDFsaves[4] is True.
-
GSASIIfiles.
ReadPowderInstprm
(instLines, bank, databanks, rd)[source]¶ Read lines from a GSAS-II (new) instrument parameter file similar to G2pwdGUI.OnLoad If instprm file has multiple banks each with header #Bank n: …, this finds matching bank no. to load - problem with nonmatches?
Note that this routine performs a similar role to
GSASIIdataGUI.GSASII.ReadPowderInstprm()
, but that will call a GUI routine for selection when needed. This routine will raise exceptions on errors and will select the first bank when a choice might be appropriate. TODO: refactor to combine the two routines.Parameters: - instLines (list) – strings from GSAS-II parameter file; can be concatenated with ‘;’
- bank (int) – bank number to check when instprm file has ‘#BANK n:…’ strings when bank = n then use parameters; otherwise skip that set. Ignored if BANK n: not present. NB: this kind of instprm file made by a Save all profile command in Instrument Par ameters
Return dict: Inst instrument parameter dict if OK, or str: Error message if failed
(transliterated from GSASIIdataGUI.py:1235 (rev 3008), function of the same name)
-
GSASIIfiles.
RereadImageData
(ImageReaderlist, imagefile, ImageTag=None, FormatName='')[source]¶ Read a single image with an image importer. This is called to reread an image after it has already been imported, so it is not necessary to reload metadata.
Based on
GetImageData.GetImageData()
which this can replace where imageOnly=TrueParameters: - ImageReaderlist (list) – list of Reader objects for images
- imagefile (str) – name of image file
- ImageTag (int/str) – specifies a particular image to be read from a file. First image is read if None (default).
- formatName (str) – the image reader formatName
Returns: an image as a numpy array
-
GSASIIfiles.
SetPowderInstParms
(Iparm, rd)[source]¶ extracts values from instrument parameters in rd.instdict or in array Iparm. Create and return the contents of the instrument parameter tree entry.
-
GSASIIfiles.
WriteControls
(filename, data)[source]¶ Write current values to a .imctrl (Image Controls) file
-
GSASIIfiles.
evalColMetadataDicts
(items, labels, lbldict, keyCols, keyExp, ShowError=False)[source]¶ Evaluate the metadata for a line in the .par file
-
GSASIIfiles.
readColMetadata
(imagefile)[source]¶ Reads image metadata from a column-oriented metadata table (1-ID style .par file). Called by
GetColumnMetadata()
The .par file has any number of columns separated by spaces. The directory for the file must be specified in Config variable
config_example.Column_Metadata_directory
. As an index to the .par file a second “label file” must be specified with the same file root name as the .par file but the extension must be .XXX_lbls (where .XXX is the extension of the image) or if that is not present extension .lbls.Parameters: imagefile (str) – the full name of the image file (with extension, directory optional) Returns: a dict with parameter values. Named parameters will have the type based on the specified Python function, named columns will be character strings The contents of the label file will look like this:
# define keywords filename:lambda x,y: "{}_{:0>6}".format(x,y)|33,34 distance: float | 75 wavelength:lambda keV: 12.398425/float(keV)|9 pixelSize:lambda x: [74.8, 74.8]|0 ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)|0,1,2,3,4 Temperature: float|53 FreePrm2: int | 34 | Free Parm2 Label # define other variables 0:day 1:month 2:date 3:time 4:year 7:I_ring
- This file contains three types of lines in any order.
- Named parameters are evaluated with user-supplied Python code (see subsequent information). Specific named parameters are used to determine values that are used for image interpretation (see table, below). Any others are copied to the Comments subsection of the Image tree item.
- Column labels are defined with a column number (integer) followed by a colon (:) and a label to be assigned to that column. All labeled columns are copied to the Image’s Comments subsection.
- Comments are any line that does not contain a colon.
Note that columns are numbered starting at zero.
Any named parameter may be defined provided it is not a valid integer, but the named parameters in the table have special meanings, as descibed. The parameter name is followed by a colon. After the colon, specify Python code that defines or specifies a function that will be called to generate a value for that parameter.
Note that several keywords, if defined in the Comments, will be found and placed in the appropriate section of the powder histogram(s)’s Sample Parameters after an integration:
Temperature
,Pressure
,Time
,FreePrm1
,FreePrm2
,FreePrm3
,Omega
,Chi
, andPhi
.After the Python code, supply a vertical bar (|) and then a list of one more more columns that will be supplied as arguments to that function.
Note that the labels for the three FreePrm items can be changed by including that label as a third item with an additional vertical bar. Labels will be ignored for any other named parameters.
The examples above are discussed here:
filename:lambda x,y: "{}_{:0>6}".format(x,y)|33,34
Here the function to be used is defined with a lambda statement:
lambda x,y: "{}_{:0>6}".format(x,y)
This function will use the format function to create a file name from the contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into the file name, followed by a underscore (_), followed by the second parameter (y, col. 34), which will be left-padded with zeros to six characters (format directive
:0>6
).When there will be more than one image generated per line in the .par file, an alternate way to generate list of file names takes into account the number of images generated:
lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
Here a third parameter is used to specify the number of images generated, where the image number is incremented for each image.
distance: float | 75
- Here the contents of column 75 will be converted to a floating point number by calling float on it. Note that the spaces here are ignored.
wavelength:lambda keV: 12.398425/float(keV)|9
- Here we define an algebraic expression to convert an energy in keV to a wavelength and pass the contents of column 9 as that input energy
pixelSize:lambda x: [74.8, 74.8]|0
- In this case the pixel size is a constant (a list of two numbers). The first column is passed as an argument as at least one argument is required, but that value is not used in the expression.
ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)|0,1,2,3,4
- This example defines a parameter that takes items in the first five columns
and formats them in a different way. This parameter is not one of the pre-defined
parameter names below. Some external code could be used to change the month string
(argument
m
) to a integer from 1 to 12. FreePrm2: int | 34 | Free Parm2 Label
- In this example, the contents of column 34 will be converted to an integer and placed as the second free-named parameter in the Sample Parameters after an integration. The label for this parameter will be changed to “Free Parm2 Label”.
Pre-defined parameter names
keyword required type Description filename yes str or list generates the file name prefix for the matching image file (MyImage001 for file /tmp/MyImage001.tif) or a list of file names. polarization no float generates the polarization expected based on the monochromator angle, defaults to 0.99. center no list of 2 floats generates the approximate beam center on the detector in mm, such as [204.8, 204.8]. distance yes float generates the distance from the sample to the detector in mm pixelSize no list of 2 floats generates the size of the pixels in microns such as [200.0, 200.0]. wavelength yes float generates the wavelength in Angstroms
4.9. GSASIImpsubs: routines used in multiprocessing¶
The routines here are called either directly when GSAS-II is used without multiprocessing or in separate cores when multiprocessing is used.
These routines are designed to be used in one of two ways:
- when multiprocessing is enabled (see global variable useMP) the computational routines are called in separate Python interpreter that is created and then deleted after use.
- when useMP is False, these routines are called directly from the main “thread”.
Note that GSASIImpsubs.InitMP()
should be called before any of the other routines
in this module are used.
-
GSASIImpsubs.
ComputePwdrProfCW
(profList)[source]¶ Compute the peaks profile for a set of CW peaks and add into the yc array
-
GSASIImpsubs.
ComputePwdrProfED
(profList)[source]¶ Compute the peaks profile for a set of TOF peaks and add into the yc array
-
GSASIImpsubs.
ComputePwdrProfPink
(profList)[source]¶ Compute the peaks profile for a set of TOF peaks and add into the yc array
-
GSASIImpsubs.
ComputePwdrProfTOF
(profList)[source]¶ Compute the peaks profile for a set of TOF peaks and add into the yc array
-
GSASIImpsubs.
InitFobsSqGlobals
(x1, ratio1, shl1, xB1, xF1, im1, lamRatio1, kRatio1, xMask1, Ka21)[source]¶ Initialize for the computation of Fobs Squared for powder histograms. Puts lots of junk into the global namespace in this module.
4.10. Module nistlat: NIST*LATTICE cell computations¶
This implements an interface to the NIST*LATTICE code using the Spring 1991 program version. NIST*LATTICE, “A Program to Analyze Lattice Relationships” was created by Vicky Lynn Karen and Alan D. Mighell (National Institute of Standards and Technology, Materials Science and Engineering Laboratory, Gaithersburg, Maryland 20899.) Minor code modifications made to provide more significant digits for cell reduction matrix terms.
Please cite V. L. Karen and A. D. Mighell, NIST Technical Note 1290 (1991), https://nvlpubs.nist.gov/nistpubs/Legacy/TN/nbstechnicalnote1290.pdf; and V. L. Karen & A. D. Mighell, U.S. Patent 5,235,523, https://patents.google.com/patent/US5235523A/en?oq=5235523 if this module is used.
This will be deployed in GSAS-II after a release of updated binary images.
-
nistlat.
CellSymSearch
(cellin, center, tolerance=[0.2, 0.2, 0.2, 1, 1, 1], mode=0, deltaV=2, output=None)[source]¶ Search for a higher symmetry lattice related to an input unit cell, and optionally to the supercells and/or subcells with a specified volume ratio to the input cell.
Parameters: - cellin (list) – six lattice constants as float values
- center (str) – cell centering code; one of P/A/B/C/F/I/R Note that ‘R’ is used for rhombohedral lattices in either hexagonal or rhombohedral (primitive) cells
- tolerance (list) – comparison tolerances for a, b, c, alpha, beta & gamma (defaults to [0.2,0.2,0.2,1.,1.,1.]
- mode (int) –
- 0: use only input cell,
- 1: generate supercells,
- 2: generate subcells
- 3: generate sub- and supercells
- deltaV (int) – volume ratios for sub/supercells if mode != 0 as ratio of original cell to smallest subcell or largest supercell to original cell. Ignored if mode=0. Otherwise should be 2, 3, 4 or 5
- output (str) – name of file to write the NIST*LATTICE output. Default is None, which does not produce a file.
Returns: a list of processed cells (only one entry in list when mode=0) where for each cell the the following items are included:
- conventional input cell;
- reduced input cell;
- symmetry-generated conventional cell;
- symmetry-generated reduced cell;
- matrix to convert sym-generated output cell to input conventional cell
-
nistlat.
CompareCell
(cell1, center1, cell2, center2, tolerance=[0.2, 0.2, 0.2, 1, 1, 1], mode='I', vrange=8, output=None)[source]¶ Search for matrices that relate two unit cells
Parameters: - cell1 (list) – six lattice constants as float values for 1st cell
- center1 (str) – cell centering code for 1st cell; one of P/A/B/C/F/I/R Note that ‘R’ is used for rhombohedral lattices in either hexagonal or rhombohedral (primitive) cells
- cell2 (list) – six lattice constants as float values for 2nd cell
- center2 (str) – cell centering code for 2nd cell (see center1)
- tolerance (list) – comparison tolerances for a, b, c, alpha, beta & gamma (defaults to [0.2,0.2,0.2,1.,1.,1.]
- mode (str) – search mode, which should be either ‘I’ or ‘F’ ‘I’ provides searching with integral matrices or ‘F’ provides searching with integral and fractional matrices
- vrange (int) – maximum matrix term range. Must be 1 <= vrange <= 10 for mode=’F’ or Must be 1 <= vrange <= 40 for mode=’I’
- output (str) – name of file to write the NIST*LATTICE output. Default is None, which does not produce a file.
Returns: A list of matrices that match cell1 to cell2 where each entry contains (det, im, m, tol, one2two, two2one) where:
- det is the determinant, giving the volume ratio between cells
- im relates the reduced cell for cell1 to the reduced cell for cell2
- m relates the reduced cell for cell2 to the reduced cell for cell1
- tol shows the quality of agreement, as six differences between the
- two reduced cells
- one2two: a numpy matrix that transforms cell1 to cell2
- two2one: a numpy matrix that transforms cell2 to cell1
-
nistlat.
ConvCell
(redcell)[source]¶ Converts a reduced cell to a conventional cell
Parameters: redcell (list) – unit cell parameters as 3 cell lengths and 3 angles (in degrees) Returns: tuple (cell,center,setting,mat) where: - cell: has the six cell dimensions for the conventional cell;
- center: is P/A/B/C/F/I/R;
- setting: is ‘ ‘ except for rhombohedral symmetry (center=R), where it will always be H (for hexagonal cell choice);
- mat: is the matrix that gives the conventional cell when the reduced cell is multiplied by mat.
-
nistlat.
ReduceCell
(center, cellin, mode=0, deltaV=0, output=None)[source]¶ Compute reduced cell(s) with NIST*LATTICE
Parameters: - center (str) – cell centering code; one of P/A/B/C/F/I/R Note that ‘R’ is used for rhombohedral lattices in either hexagonal or rhombohedral (primitive) cells
- cellin (list) – six lattice constants as float values
- mode (int) –
- 0: reduction,
- 1: generate supercells,
- 2: generate subcells
- 3: generate sub- and supercells
- deltaV (int) – volume ratios for sub/supercells if mode != 0 as ratio of original cell to smallest subcell or largest supercell to original cell. Ignored if mode=0. Otherwise should be 2, 3, 4 or 5
- output (str) – name of file to write the NIST*LATTICE output. Default is None, which does not produce a file.
Returns: a dict with two items, ‘input’ and ‘output’. The value for ‘input’ is the input cell as (cell,center,setting). The value for ‘output’ is a list of reduced cells of form (d,cell,vol,mat,center,setting). In these:
- cell: a list with the six cell dimensions;
- center: is as above (always ‘P’ on output);
- setting: is ‘ ‘ except for rhombohedral symmetry where it may be R or H for the cell type;
- d: is the volume ratio for new cell over input cell;
- vol: is volume of output cell
- mat: is the matrix that gives the output cell when the input cell is multiplied by mat.
-
nistlat.
showCell
(cell, center='P', setting=' ', *ignored)[source]¶ show unit cell input or output nicely formatted.
Parameters: - cell (list) – six lattice constants as float values; a 7th volume value is ignored if present.
- center (str) – cell centering code; one of P/A/B/C/F/I/R Note that ‘R’ is used for rhombohedral lattices in either rhombohedral (primitive) or hexagonal cells.
- setting (str) – is ‘ ‘ except for rhombohedral symmetry where it will be R or H for the cell type.
Returns: a formatted string
-
nistlat.
uniqCells
(cellList)[source]¶ remove duplicated cells from a cell output list from
ReduceCell()
Parameters: cellList (list) – A list of reduced cells where each entry represents a reduced cell as (_,cell,_,_,center,…) where cell has six lattice constants and center is the cell centering code (P/A/B/C/F/I/R). Returns: a list as above, but where each unique cell is listed only once
4.11. ElementTable: Periodic Table Data¶
Element table data for building periodic table with valences & JMOL colors. Need these in case we go back to this periodic table coloring scheme.
Defines list ElTable
which contains all defined oxidation states for each
element, the location in the table, an element name, a color, a size and a
second color.
4.12. FormFactors: Scattering Data¶
Contains atomic scattering factors from “New Analytical Scattering Factor Functions for Free Atoms and Ions for Free Atoms and Ions”, D. Waasmaier & A. Kirfel, Acta Cryst. (1995). A51, 416-413.
Also, tabulated coefficients for calculation of Compton Cross Section as a function of sin(theta)/lambda from “Analytic Approximations to Incoherently Scattered X-Ray Intensities”, H. H. M. Balyuzi, Acta Cryst. (1975). A31, 600.
4.13. ImageCalibrants: Calibration Standards¶
GSASII powder calibrants in dictionary ImageCalibrants.Calibrants
containing substances commonly used for powder calibrations for image data.
Each entry in ImageCalibrants
consists of:
'key':([Bravais num,],[space group,],[(a,b,c,alpha,beta,gamma),],no. lines skipped,(dmin,pixLimit,cutOff),(absent list))
* See below for Bravais num assignments.
* The space group may be an empty string.
* The absent list is optional; it gives indices of lines that have no intensity despite being allowed - see the Si example below; counting begins at zero
As an example:
'LaB6 SRM660a':([2,],['',][(4.1569162,4.1569162,4.1569162,90,90,90),],0,(1.0,10,10.)),
For calibrants that are mixtures, the “Bravais num” and “(a,b,…)” values are repeated, as in this case:
'LaB6 & CeO2':([2,0],['',''] [(4.1569,4.1569,4.1569,90,90,90),(5.4117,5.4117,5.4117,90,90,90)], 0, (1.0,2,1.)),
Note that Si has reflections (the 4th, 11th,…) that are not extinct by symmetry but still have zero intensity. These are supplied in the final list:
'Si':([0,],['F d 3 m'],[(5.4311946,5.4311946,5.4311946,90,90,90),],0,(1.,10,10.),(3,10,13,20,23,26,33,35,40,43)),
- Note, the Bravais numbers are:
- 0 F cubic
- 1 I cubic
- 2 P cubic
- 3 R hexagonal (trigonal not rhombohedral)
- 4 P hexagonal
- 5 I tetragonal
- 6 P tetragonal
- 7 F orthorhombic
- 8 I orthorhombic
- 9 C orthorhombic
- 10 P orthorhombic
- 11 C monoclinic
- 12 P monoclinic
- 13 P triclinic
4.13.1. User-Defined Calibrants¶
To expand this list with locally needed additions, do not modify this
ImageCalibrants.py
file,
because you may lose these changes during a software update. Instead
duplicate the format of this file in a file named UserCalibrants.py
and there define the material(s) you want:
Calibrants={
'LaB6 skip 2 lines':([2,],['',],[(4.1569162,4.1569162,4.1569162,90,90,90),],2,(1.0,10,10),()),
}
New key values will be added to the list of options.
If a key is duplicated, the information in UserCalibrants.py
will
override the entry in this (the ImageCalibrants.py
file).
4.14. atmdata: Table of atomic data¶
The entries here are:
XrayFF: a dict of form factor coefficients
AtmSize: atom Sizes, bond radii, angle radii, H-bond radii
AtmBlens: atom masses & neutron scattering length (b,b’), sig(incoh) @ 1A
MagFF: neutron magnetic form factor coeff: M for j<0> & N for j<2>
Sources:
Exponential scattering factor curve coeficients, Cromer and Waber(1971) Int. Tables Vol. IV. Delta f’ and delta f” terms calcd via D.T. Cromer & D.A. Liberman (1981), Acta Cryst. A37, 267-268. Atomic weights from CRC 56th Edition
Electron scattering factor curve coefficients from International Tables for Crystallography, Vol. C, Ch 4. Sect. 4.3.2.
Neutron scattering lengths & abs. cross sections from H. Rauch & W. Waschowski, Neutron Data Booklet, 2003. X-ray <j0> & <j2> coeff. from Intl. Tables for Cryst, Vol. C 5-d <j0> & <j2> from Kobayashi K, Nagao T, Ito M. Acta Crystallogr A67, 473-480 (2011)
Neutron anomalous coeff (LS) from fitting Lynn & Seeger, At. Data & Nuc. Data Tables, 44, 191-207(1990)
O2- x-ray scattering factor from Tokonami (1965) Acta Cryst 19, 486
At wts from 14th ed Nuclides & Isotopes, 1989 GE Co.
4.15. defaultIparms: Table of instrument parameters¶
Defines some default instrument parameters. Format for each is a list of strings finished with a ‘ ‘. Begin with ‘#GSAS-II…’ as the reader routine checks this. Each line can be comprised of a block of ‘;’ delimited name:value pairs. All instrument parameters must be included; even those = 0. Use a GSAS-II instprm file as a source for the entries.
For a new entry:
Append a useful name to defaultIparms_lbl.
Append the list of lines to defaultIparms.
defaultIparm_lbl: defines a list of labels.
defaultIparms: defines a list of multiple strings with values for each set of defaults.