' + _('Hide Search Matches') + '
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').appendTo(this.out); + this.dots = $('').appendTo(this.title); + this.status = $('').appendTo(this.out); + this.output = $('\
+ \
+
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+ ';
+
+ var replyTemplate = '\
+ \
+
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+ \
+ \ + <%username%>\ + \ + <%time.delta%>\ +
\ +<#text#>
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+ \ + \ + reply ▿\ + proposal ▹\ + \ + \ + \ +
\ +\ +<#proposal_diff#>\ +\ +
+
+
+
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+
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diff --git a/api/diffpy.Structure.Parsers.html b/api/diffpy.Structure.Parsers.html
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+ diffpy API¶
+
+
+-
+
- Structure Package
-
+
- Structure Package +
- SpaceGroups Module +
- StructureErrors Module +
- SymmetryUtilities Module +
- atom Module +
- bratomsstructure Module +
- lattice Module +
- mmlibspacegroups Module +
- pdffitstructure Module +
- sgtbxspacegroups Module +
- spacegroupmod Module +
- structure Module +
- utils Module +
- version Module +
- Subpackages
-
+
- Parsers Package + +
- applications Package + +
- expansion Package + +
- tests Package + +
+
+
+
+
+
+
+
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diff --git a/api/diffpy.Structure.applications.html b/api/diffpy.Structure.applications.html
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+
+ Parsers Package¶
+
+
+Parsers Package¶
+Conversion plugins for various structure formats
+The recognized structure formats are defined by subclassing StructureParser, +by convention these classes are named P_<format>. The parser classes should +to override the parseLines() and toLines() methods of StructureParser. +Any structure parser needs to be registered in parser_index module.
+For normal usage it should be sufficient to use the routines provided +in this module.
+-
+
- Content: +
- StructureParser – base class for concrete Parsers +parser_index – dictionary of known structure formats +getParser – factory for Parser at given format +inputFormats – list of available input formats +outputFormats – list of available output formats +
-
+
- +diffpy.Structure.Parsers.getParser(format)¶ +
Return Parser instance for a given structure format. +Raises StructureFormatError exception when format is not defined.
+
-
+
- +diffpy.Structure.Parsers.inputFormats()¶ +
Return list of implemented input structure formats
+
-
+
- +diffpy.Structure.Parsers.outputFormats()¶ +
return list of implemented output structure formats
+
+
+P_auto Module¶
+Parser for automatic file format detection
+This Parser does not provide the the toLines() method.
+-
+
- +class diffpy.Structure.Parsers.P_auto.P_auto¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser with automatic detection of structure format. +When successful, it sets its format attribute to detected +structure format.
+-
+
- +parse(s)¶ +
Detect format and create Structure instance from a string. +Set format attribute to the detected file format.
+Return Structure object or raise StructureFormatError exception.
+
-
+
- +parseFile(filename)¶ +
Detect format and create Structure instance from an existing file. +Set format attribute to the detected file format.
+filename – path to structure file
+Return Structure object. +Raise StructureFormatError or IOError.
+
-
+
- +parseLines(lines)¶ +
Detect format and create Structure instance from a list of lines. +Set format attribute to the detected file format.
+Return Structure object or raise StructureFormatError exception.
+
-
+
- +diffpy.Structure.Parsers.P_auto.getParser()¶ +
+
+P_bratoms Module¶
+Parser for Bruce Ravel’s Atoms structure format
+-
+
- +class diffpy.Structure.Parsers.P_bratoms.P_bratoms¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser for Bruce Ravel’s Atoms structure format.
+-
+
- +parseLines(lines)¶ +
Parse list of lines in atoms format.
+Return Structure object or raise StructureFormatError.
+
-
+
- +plist = ['a', 'b', 'c', 'alpha', 'beta', 'gamma']¶ +
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in PDFfit format.
+Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_bratoms.getParser()¶ +
+
+P_cif Module¶
+Parser for basic CIF file format
+http://www.iucr.org/iucr-top/cif/home.html
+-
+
- +class diffpy.Structure.Parsers.P_cif.P_cif¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Simple parser for CIF structure format. +Reads Structure from the first block containing _atom_site_label key. +Following blocks, if any are ignored.
+Data members:
+format – structure format name +ciffile – instance of CifFile from PyCifRW +stru – Structure instance used for cif input or output
+Data members used for input only:
+spacegroup – instance of SpaceGroup used for symmetry expansion +eau – instance of ExpandAsymmetricUnit from SymmetryUtilities +asymmetric_unit – list of atom instances for the original asymmetric
++
+unit in the CIF file-
+
- labelindex – dictionary mapping unique atom label to index of atom +
- in self.asymmetric_unit +
- cif_sgname – space group name obtained by looking up the value of +
- _space_group_name_Hall, _symmetry_space_group_name_Hall, +_space_group_name_H-M_alt, _symmetry_space_group_name_H-M +items. None when neither is defined. +
-
+
- +BtoU = 0.012665147955292222¶ +
-
+
- +parse(s)¶ +
Create Structure instance from a string in CIF format.
+Return Structure instance or raise StructureFormatError.
+
-
+
- +parseFile(filename)¶ +
Create Structure from an existing CIF file.
+filename – path to structure file
+Return Structure object. +Raise StructureFormatError or IOError.
+
-
+
- +parseLines(lines)¶ +
Parse list of lines in CIF format.
+lines – list of strings stripped of line terminator
+Return Structure instance or raise StructureFormatError.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in basic CIF format.
+Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_cif.fixIfWindowsPath(filename)¶ +
Convert Windows-style path to valid local URL. +CifFile loads files using urlopen, which fails for Windows-style paths.
+filename – path to be fixed
+Return fixed URL when run on Windows, otherwise return filename.
+
-
+
- +diffpy.Structure.Parsers.P_cif.getParser()¶ +
-
+
- +diffpy.Structure.Parsers.P_cif.getSymOp(s)¶ +
Create SpaceGroups.SymOp instance from a string.
+s – formula for equivalent coordinates, for example ‘x,1/2-y,1/2+z’
+Return instance of SymOp.
+
-
+
- +diffpy.Structure.Parsers.P_cif.leading_float(s)¶ +
Obtain first float from a string and ignore any trailing characters. +Useful for extracting values from “value(std)” syntax.
+Return float.
+
+
+P_discus Module¶
+Parser for DISCUS structure format
+-
+
- +class diffpy.Structure.Parsers.P_discus.P_discus¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser for DISCUS structure format. The parser chokes +on molecule and generator records.
+-
+
- +parseLines(lines)¶ +
Parse list of lines in DISCUS format.
+Return PDFFitStructure instance or raise StructureFormatError.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in DISCUS format. +Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_discus.getParser()¶ +
+
+P_pdb Module¶
+Basic parser for PDB structure format.
+References
+++
-
+
- +class diffpy.Structure.Parsers.P_pdb.P_pdb¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Simple parser for PDB format. +The parser understands following PDB records: TITLE, CRYST1, SCALE1, +SCALE2, SCALE3, ATOM, SIGATM, ANISOU, SIGUIJ, TER, HETATM, END
+Static data members:
+orderOfRecords – order of PDB record labels +validRecords – dictionary of valid PDB records
+-
+
- +atomLines(stru, idx)¶ +
build ATOM records and possibly SIGATM, ANISOU or SIGUIJ records +for structure stru atom number aidx
+
-
+
- +cryst1Lines(stru)¶ +
build lines corresponding to CRYST1 record
+
-
+
- +orderOfRecords = ['HEADER', 'OBSLTE', 'TITLE', 'CAVEAT', 'COMPND', 'SOURCE', 'KEYWDS', 'EXPDTA', 'AUTHOR', 'REVDAT', 'SPRSDE', 'JRNL', 'REMARK', 'REMARK', 'REMARK', 'REMARK', 'DBREF', 'SEQADV', 'SEQRES', 'MODRES', 'HET', 'HETNAM', 'HETSYN', 'FORMUL', 'HELIX', 'SHEET', 'TURN', 'SSBOND', 'LINK', 'HYDBND', 'SLTBRG', 'CISPEP', 'SITE', 'CRYST1', 'ORIGX1', 'ORIGX2', 'ORIGX3', 'SCALE1', 'SCALE2', 'SCALE3', 'MTRIX1', 'MTRIX2', 'MTRIX3', 'TVECT', 'MODEL', 'ATOM', 'SIGATM', 'ANISOU', 'SIGUIJ', 'TER', 'HETATM', 'ENDMDL', 'CONECT', 'MASTER', 'END']¶ +
-
+
- +parseLines(lines)¶ +
Parse list of lines in PDB format.
+Return Structure instance or raise StructureFormatError.
+
-
+
- +titleLines(stru)¶ +
build lines corresponding to TITLE record
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in PDFFit format.
+Return list of strings.
+
-
+
- +validRecords = {'KEYWDS': None, 'SEQRES': None, 'DBREF': None, 'TITLE': None, 'ORIGX1': None, 'ENDMDL': None, 'HETSYN': None, 'SIGATM': None, 'LINK': None, 'HELIX': None, 'MTRIX1': None, 'END': None, 'MODEL': None, 'ANISOU': None, 'SLTBRG': None, 'REMARK': None, 'SCALE1': None, 'SCALE2': None, 'AUTHOR': None, 'CRYST1': None, 'SIGUIJ': None, 'CISPEP': None, 'ORIGX3': None, 'ORIGX2': None, 'MODRES': None, 'SOURCE': None, 'FORMUL': None, 'MASTER': None, 'CAVEAT': None, 'SPRSDE': None, 'COMPND': None, 'TER': None, 'REVDAT': None, 'SSBOND': None, 'HET': None, 'OBSLTE': None, 'CONECT': None, 'SHEET': None, 'TVECT': None, 'HETNAM': None, 'SITE': None, 'HEADER': None, 'ATOM': None, 'HYDBND': None, 'EXPDTA': None, 'SCALE3': None, 'HETATM': None, 'TURN': None, 'JRNL': None, 'MTRIX2': None, 'SEQADV': None, 'MTRIX3': None}¶ +
-
+
- +diffpy.Structure.Parsers.P_pdb.getParser()¶ +
+
+P_pdffit Module¶
+Parser for PDFfit structure format
+-
+
- +class diffpy.Structure.Parsers.P_pdffit.P_pdffit¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser for PDFfit structure format.
+stru – Structure instance used for cif input or output
+-
+
- +parseLines(lines)¶ +
Parse list of lines in PDFfit format.
+Return Structure object or raise StructureFormatError.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in PDFfit format.
+Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_pdffit.getParser()¶ +
+
+P_rawxyz Module¶
+Parser for raw XYZ file format. Raw XYZ is a 3 or 4 column text +file with cartesian coordinates of atoms and an optional first column +for atom types.
+-
+
- +class diffpy.Structure.Parsers.P_rawxyz.P_rawxyz¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser –> StructureParser subclass for RAWXYZ format
+-
+
- +parseLines(lines)¶ +
Parse list of lines in RAWXYZ format.
+Return Structure object or raise StructureFormatError.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in XYZ format.
+Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_rawxyz.getParser()¶ +
+
+P_xcfg Module¶
+Parser for extended CFG format used by atomeye
+-
+
- +class diffpy.Structure.Parsers.P_xcfg.P_xcfg¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser for AtomEye extended CFG format.
+-
+
- cluster_boundary – width of boundary around corners of non-periodic +
- cluster to avoid PBC effects in atomeye +
-
+
- +cluster_boundary = 2¶ +
-
+
- +parseLines(lines)¶ +
Parse list of lines in PDB format.
+Return Structure object or raise StructureFormatError.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in XCFG atomeye format.
+Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_xcfg.getParser()¶ +
+
+P_xyz Module¶
+Parser for XYZ file format, where +first line gives number of atoms +second one has optional title +remaining lines contain element, x, y, z
+-
+
- +class diffpy.Structure.Parsers.P_xyz.P_xyz¶ +
Bases: diffpy.Structure.Parsers.structureparser.StructureParser
+Parser for standard XYZ structure format.
+-
+
- +parseLines(lines)¶ +
Parse list of lines in XYZ format.
+Return Structure object or raise StructureFormatError.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines in XYZ format.
+Return list of strings.
+
-
+
- +diffpy.Structure.Parsers.P_xyz.getParser()¶ +
+
+parser_index_mod Module¶
+Index of recognized structure formats, their IO capabilities and +associated modules where they are defined. Plugins for new structure +formats need to be added to the parser_index dictionary in this module.
+
+
+structureparser Module¶
+Definition of StructureParser, a base class for specific parsers.
+-
+
- +class diffpy.Structure.Parsers.structureparser.StructureParser¶ +
Bases: object
+Base class for all structure parsers.
+-
+
- Data members: +
- format – format of particular parser +filename – path to structure file that is read or written +
-
+
- +parse(s)¶ +
Create Structure instance from a string.
+Return Structure object or raise StructureFormatError exception.
+
-
+
- +parseFile(filename)¶ +
Create Structure instance from an existing file.
+filename – path to structure file
+Return Structure object. +Raise StructureFormatError or IOError.
+
-
+
- +parseLines(lines)¶ +
Create Structure instance from a list of lines.
+Return Structure object or raise StructureFormatError exception. +This method has to be overloaded in derived class.
+
-
+
- +toLines(stru)¶ +
Convert Structure stru to a list of lines. +This method has to be overloaded in derived class.
+Return list of strings.
+
-
+
- +tostring(stru)¶ +
Convert Structure instance to a string.
+
+
+
+
+
+
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diff --git a/api/diffpy.Structure.expansion.html b/api/diffpy.Structure.expansion.html
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+
+ applications Package¶
+
+
+applications Package¶
+Script applications that use the diffpy.Structure package.
+
+
+anyeye Module¶
+anyeye view structure file in atomeye +Usage: anyeye [options] strufile
+anyeye understands more structure formats than atomeye. It converts strufile +to a temporary XCFG file which is opened in atomeye. Supported file formats:
+++inputFormats
-
+
- Options: +
+
++ + + +-f, --formula +override chemical formula in strufile, formula defines +elements in the same order as in strufile, e.g, Na4Cl4 +-w, --watch +watch input file for changes +--viewer=VIEWER +the structure viewer program, by default “atomeye”. +The program will be executed as “VIEWER structurefile” -
+
- –formats=FORMATS comma separated list of file formats that are understood +
- by the VIEWER, by default “xcfg,pdb”. Files of other +formats will be converted to the first listed format. +
+
++ + + +-h, --help +display this message and exit +-V, --version +show script version and exit
+
-
+
- +diffpy.Structure.applications.anyeye.cleanUp(pd)¶ +
-
+
- +diffpy.Structure.applications.anyeye.convertStructureFile(pd)¶ +
-
+
- +diffpy.Structure.applications.anyeye.die(exit_status=0, pd={})¶ +
-
+
- +diffpy.Structure.applications.anyeye.loadStructureFile(filename, format='auto')¶ +
Load structure from specified file.
+Return a tuple of (Structure, fileformat).
+
-
+
- +diffpy.Structure.applications.anyeye.main()¶ +
-
+
- +diffpy.Structure.applications.anyeye.parseFormula(formula)¶ +
parse chemical formula and return a list of elements
+
-
+
- +diffpy.Structure.applications.anyeye.signalHandler(signum, stackframe)¶ +
-
+
- +diffpy.Structure.applications.anyeye.usage(style=None)¶ +
show usage info, for style==”brief” show only first 2 lines
+
-
+
- +diffpy.Structure.applications.anyeye.version()¶ +
-
+
- +diffpy.Structure.applications.anyeye.watchStructureFile(pd)¶ +
+
+transtru Module¶
+transtru translate structure file to different format +Usage: transtru INFMT..OUTFMT strufile
+translates structure file strufile from INFMT to OUTFMT format and prints it +to the screen. Use “-” as strufile to read from standard input. To save the +translated file, use
+++transtru INFMT..OUTFMT strufile > strufile.out
-
+
- Supported input and output structure formats are +
- INFMT: inputFormats +OUTFMT: outputFormats +
- Options: +
+
++ + + +-h, --help +display this message +-V, --version +show script version
+
-
+
- +diffpy.Structure.applications.transtru.main()¶ +
-
+
- +diffpy.Structure.applications.transtru.usage(style=None)¶ +
show usage info, for style==”brief” show only first 2 lines
+
-
+
- +diffpy.Structure.applications.transtru.version()¶ +
+
+
+
+
+
\ No newline at end of file
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+ expansion Package¶
+
+
+expansion Package¶
+Methods and classes for manipulating Structure instances.
+Package content:
+supercell – create a supercell from an existing Structure.
+
+
+makeCuboctahedron Module¶
+Make a spheroid nanoparticle from a template structure.
+-
+
- +diffpy.Structure.expansion.makeCuboctahedron.makeCuboctahedron(S, dist)¶ +
Make a cuboctahedron nanoparticle.
+Arguments +S – A Structure instance +dist – Distance from center to nearest face
+Returns a new structure instance
+
+
+makeEllipsoid Module¶
+Make a spheroid nanoparticle from a template structure.
+-
+
- +diffpy.Structure.expansion.makeEllipsoid.makeEllipsoid(S, a, b=None, c=None)¶ +
Cut a structure out of another one.
+Arguments +S – A Structure instance +a – primary equatorial radius (along x-axis) +b – secondary equatorial radius (along y-axis). If b is None
++
+(default) then it is set equal to a-
+
- c – polar radius (along z-axis). If c is None (default), then it is +
- set equal to a. +
Returns a new structure instance
+
-
+
- +diffpy.Structure.expansion.makeEllipsoid.makeSphere(S, radius)¶ +
Create a spherical nanoparticle.
+Arguments +S – A Structure instance +radius – primary equatorial radius (along x-axis)
+Returns a new structure instance
+
+
+shapeUtils Module¶
+Utilities for making shapes.
+-
+
- +diffpy.Structure.expansion.shapeUtils.findCenter(S)¶ +
Find the approximate center atom of a structure.
+The center of the structure is the atom closest to (0.5, 0.5, 0.5)
+Returns the index of the atom.
+
+
+supercell_mod Module¶
+This module contains functions for simple structure manipulation.
+-
+
- +diffpy.Structure.expansion.supercell_mod.supercell(S, mno)¶ +
Perform supercell expansion for a structure.
+New lattice parameters are multiplied and fractional coordinates +divided by corresponding multiplier. New atoms are grouped with +their source in the original cell.
+S – an instance of Structure from diffpy.Structure. +mno – sequence of 3 integers for cell multipliers along
++
+the a, b and c axes.Return a new expanded structure instance. +Raise TypeError when S is not Structure instance. +Raise ValueError for invalid mno argument.
+
+
+
+
+
+
\ No newline at end of file
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Structure Package¶
+
+
+Structure Package¶
+classes related to structure of materials +Classes:
+++Atom +Lattice +Structure +PDFFitStructure
-
+
- Exceptions: +
- StructureFormatError +LatticeError +SymmetryError +IsotropyError +
-
+
- +diffpy.Structure.loadStructure(filename, fmt='auto')¶ +
Load a new structure from a specified file.
+filename – file to be loaded +fmt – format of the structure file. Must be one of the formats
++
+defined in the Parsers subpackage. When ‘auto’, all +Parsers are tried in sequence.Return a new Structure object. +Return PDFFitStructure object for ‘pdffit’ or ‘discus’ formats.
+
-
+
- +diffpy.Structure.test()¶ +
Execute all unit tests for the diffpy.Structure package. +Return a unittest TestResult object.
+
+
+SpaceGroups Module¶
+Space group classes and definitions from mmLib and sgtbx.
+-
+
- +diffpy.Structure.SpaceGroups.GetSpaceGroup(sgid)¶ +
Returns the SpaceGroup instance for the given identifier.
+-
+
- sgid – space group symbol, either short_name or pdb_name, +
- whatever it means in mmlib. Can be also an integer. +
Return space group instance. +Raise ValueError when not found.
+
-
+
- +diffpy.Structure.SpaceGroups.IsSpaceGroupIdentifier(sgid)¶ +
Check if identifier can be used as an argument to GetSpaceGroup.
+Return bool.
+
+
+StructureErrors Module¶
+Exceptions used in Structure package.
+-
+
- +exception diffpy.Structure.StructureErrors.IsotropyError¶ +
Bases: exceptions.Exception
+Exception raised for invalid operations on isotropic atoms.
+
-
+
- +exception diffpy.Structure.StructureErrors.LatticeError¶ +
Bases: exceptions.Exception
+Exception for impossible lattice parameters.
+
-
+
- +exception diffpy.Structure.StructureErrors.StructureFormatError¶ +
Bases: exceptions.Exception
+Exception for failed IO from Structure file
+
-
+
- +exception diffpy.Structure.StructureErrors.SymmetryError¶ +
Bases: exceptions.Exception
+Exception raised for invalid symmetry operations.
+
+
+SymmetryUtilities Module¶
+Symmetry utility functions such as expansion of asymmetric unit, +and generation of positional constraints.
+-
+
- +class diffpy.Structure.SymmetryUtilities.ExpandAsymmetricUnit(spacegroup, corepos, coreUijs=None, sgoffset=[0, 0, 0], eps=1e-05)¶ +
Bases: object
+Expand asymmetric unit and anisotropic thermal displacement
+-
+
- Data members: +
spacegroup – instance of SpaceGroup +corepos – list of positions in asymmetric unit,
++
+it may contain duplicatescoreUijs – thermal factors for corepos (defaults to zeros) +sgoffset – optional offset of space group origin [0, 0, 0] +eps – cutoff for equivalent positions
+
+- Calculated data members: +
- multiplicity – multiplicity of each site in corepos +Uisotropy – bool flags for isotropic sites in corepos +expandedpos – list of equivalent positions per each site in corepos +expandedUijs – list of thermal factors per each site in corepos +
-
+
- +GeneratorSite(spacegroup, xyz, Uij=array([[ 0., 0., 0.], +
- +[ 0., 0., 0.], +
- +[ 0., 0., 0.]]), sgoffset=[0, 0, 0], eps=1e-05) +
Bases: object
+Storage of data related to a generator positions.
+-
+
- Data members: +
xyz – fractional coordinates of generator site +Uij – anisotropic thermal displacement at generator site +sgoffset – offset of space group origin [0, 0, 0] +eps – cutoff for equal positions +eqxyz – list of equivalent positions +eqUij – list of displacement matrices at equivalent positions +symops – nested list of operations per each eqxyz +multiplicity – generator site multiplicity +Uisotropy – bool flag for isotropic thermal factors +invariants – list of invariant operations for generator site +null_space – null space of all possible differences of invariant
++
+rotational matrices, this is a base of symmetry +allowed shifts.Uspace – 3D array of independent components of U matrices. +pparameters – list of (xyz symbol, value) pairs +Uparameters – list of (U symbol, value) pairs
+
+
-
+
- +GeneratorSite.UFormula(pos, Usymbols=['U11', 'U22', 'U33', 'U12', 'U13', 'U23'])¶ +
List of atom displacement formulas with custom parameter symbols.
+pos – fractional coordinates of possibly equivalent site +Usymbols – 6 symbols for possible U matrix parameters
+Return U element formulas in a dictionary where keys are from +(‘U11’,’U22’,’U33’,’U12’,’U13’,’U23’) or empty dictionary when +pos is not equivalent to generator.
+
-
+
- +GeneratorSite.Ucomponents = array([[[ 1., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.]], [[ 0., 0., 0.], [ 0., 1., 0.], [ 0., 0., 0.]], [[ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 1.]], [[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 0.]], [[ 0., 0., 1.], [ 0., 0., 0.], [ 1., 0., 0.]], [[ 0., 0., 0.], [ 0., 0., 1.], [ 0., 1., 0.]]])¶ +
-
+
- +GeneratorSite.eqIndex(pos)¶ +
Index of the nearest generator equivalent site
+pos – fractional coordinates
+Return integer.
+
-
+
- +GeneratorSite.idx2Usymbol = {0: 'U11', 1: 'U12', 2: 'U13', 3: 'U12', 4: 'U22', 5: 'U23', 6: 'U13', 7: 'U23', 8: 'U33'}¶ +
-
+
- +GeneratorSite.positionFormula(pos, xyzsymbols=('x', 'y', 'z'))¶ +
Formula of equivalent position with respect to generator site
+pos – fractional coordinates of possibly equivalent site +xyzsymbols – symbols for parametrized coordinates
+Return position formulas in a dictionary with keys equal (“x”, “y”, “z”) +or an empty dictionary when pos is not equivalent to generator. +Formulas are formatted as “[[-][%g*]{x|y|z}] [{+|-}%g]”, for example +“-x”, “z +0.5”, “0.25”.
+
-
+
- +GeneratorSite.signedRatStr(x)¶ +
Convert floating point number to signed rational representation. +Possible fractional are multiples of 1/3, 1/6, 1/7, 1/9, if these +are not close, return “%+g” format.
+Return string.
+
-
+
- +class diffpy.Structure.SymmetryUtilities.SymmetryConstraints(spacegroup, positions, Uijs=None, sgoffset=[0, 0, 0], eps=1e-05)¶ +
Bases: object
+Generate symmetry constraints for specified positions
+-
+
- Data members: +
- spacegroup – instance of SpaceGroup +positions – all positions to be constrained +Uijs – thermal factors for all positions (defaults to zeros) +sgoffset – optional offset of space group origin [0, 0, 0] +eps – cutoff for equivalent positions +
- Calculated data members: +
corepos – list of of positions in the asymmetric unit +coremap – dictionary mapping indices of asymmetric core positions
++
+to indices of all symmetry related positions-
+
- poseqns – list of coordinate formula dictionaries per each site. +
- Formula dictionary keys are from (“x”, “y”, “z”) and +the values are formatted as [[-]{x|y|z}%i] [{+|-}%g], +for example: “x0”, “-x3”, “z7 +0.5”, “0.25”. +
pospars – list of (xyz symbol, value) pairs +Ueqns – list of anisotropic atomic displacement formula
++
+dictionaries per each position. Formula dictionary +keys are from (‘U11’,’U22’,’U33’,’U12’,’U13’,’U23’) +and the values are formatted as {[%g*][Uij%i]|0}, +for example: “U110”, “0.5*U2213”, “0”Upars – list of (U symbol, value) pairs +Uisotropy – list of bool flags for isotropic thermal displacements
+
+
-
+
- +UFormulas(Usymbols=None)¶ +
List of atom displacement formulas with custom parameter symbols.
+Usymbols – list of custom symbols used in formula strings
+Return list of atom displacement formula dictionaries per each site. +Formula dictionary keys are from (‘U11’,’U22’,’U33’,’U12’,’U13’,’U23’) +and the values are formatted as {[%g*][Usymbol]|0}, for example: +“U11”, “0.5*@37”, “0”.
+
-
+
- +UFormulasPruned(Usymbols=None)¶ +
List of atom displacement formula dictionaries with constant items +removed. See also UFormulas().
+Usymbols – list of custom symbols used in formula strings
+Return list of atom displacement formulas in tuples of +(U11, U22, U33, U12, U13, U23).
+
-
+
- +UparSymbols()¶ +
Return list of standard atom displacement parameter symbols.
+
-
+
- +UparValues()¶ +
Return list of atom displacement parameters values.
+
-
+
- +positionFormulas(xyzsymbols=None)¶ +
List of position formulas with custom parameter symbols.
+xyzsymbols – list of custom symbols used in formula strings
+Return list of coordinate formulas dictionaries. Formulas dictionary +keys are from (“x”, “y”, “z”) and the values are formatted as +[[-]{symbol}] [{+|-}%g], for example: “x0”, “-sym”, “@7 +0.5”, “0.25”.
+
-
+
- +positionFormulasPruned(xyzsymbols=None)¶ +
List of position formula dictionaries with constant items removed. +See also positionFormulas().
+xyzsymbols – list of custom symbols used in formula strings
+Return list of coordinate formula dictionaries.
+
-
+
- +posparSymbols()¶ +
Return list of standard position parameter symbols.
+
-
+
- +posparValues()¶ +
Return list of position parameters values.
+
-
+
- +diffpy.Structure.SymmetryUtilities.equalPositions(xyz0, xyz1, eps=1e-05)¶ +
Equality of two coordinates with optional tolerance.
+xyz0, xyz1 – fractional coordinates +eps – tolerance for equality of coordinates
+Return bool.
+
-
+
- +diffpy.Structure.SymmetryUtilities.expandPosition(spacegroup, xyz, sgoffset=[0, 0, 0], eps=1e-05)¶ +
Obtain unique equivalent positions and corresponding operations.
+spacegroup – instance of SpaceGroup +xyz – position to be expanded +sgoffset – offset of space group origin [0, 0, 0] +eps – cutoff for equal positions
+Return a tuple with (list of unique equivalent positions, nested +list of SpaceGroups.SymOp instances, site multiplicity).
+
-
+
- +diffpy.Structure.SymmetryUtilities.isSpaceGroupLatPar(spacegroup, a, b, c, alpha, beta, gamma)¶ +
Check if space group allows passed lattice parameters.
+spacegroup – instance of SpaceGroup +a, b, c, alpha, beta, gamma – lattice parameters
+Return bool.
+
-
+
- +diffpy.Structure.SymmetryUtilities.isconstantFormula(s)¶ +
Check if formula string is constant. True when argument +is a floating point number or a fraction of float with integer.
+s – formula string
+Return bool.
+
-
+
- +diffpy.Structure.SymmetryUtilities.nearestSiteIndex(sites, xyz)¶ +
Index of the nearest site to a specified position.
+sites – list of coordinates or a 2-dimensional numpy.array +xyz – single position
+Return integer.
+
-
+
- +diffpy.Structure.SymmetryUtilities.nullSpace(A)¶ +
Null space of matrix A.
+
-
+
- +diffpy.Structure.SymmetryUtilities.positionDifference(xyz0, xyz1)¶ +
Smallest difference between two coordinates in periodic lattice.
+xyz0, xyz1 – fractional coordinates
+Return dxyz, a numpy.array dxyz with 0 <= dxyz <= 0.5.
+
-
+
- +diffpy.Structure.SymmetryUtilities.pruneFormulaDictionary(eqdict)¶ +
Remove constant items from formula dictionary.
+-
+
- eqdict – formula dictionary which maps standard variable symbols +
- (“x”, “U11”) to string formulas (“0”, “-x3”, “z7 +0.5”) +
Return pruned formula dictionary.
+
+
+atom Module¶
+class Atom for storing properties of a single atom
+-
+
- +class diffpy.Structure.atom.Atom(atype=None, xyz=None, label=None, occupancy=None, anisotropy=None, U=None, Uisoequiv=None, lattice=None)¶ +
Bases: object
+Atom –> class for storing atom information
+-
+
- Data members: +
element – type of the atom +xyz – fractional coordinates, numpy array +x, y, z – fractional coordiantes, float properties synced with xyz +label – string atom label +occupancy – fractional occupancy +xyz_cartn – absolute Cartesian coordinates, property synced with xyz +anisotropy – flag for anisotropic thermal displacements, property +U – anisotropic thermal displacement tensor, property +Uij – elements of U tensor, where i, j are from (1, 2, 3),
++
+property-
+
- Uisoequiv – isotropic thermal displacement or equivalent value, +
- property +
- Bisoequiv – Debye-Waler isotropic temperature factor or equivalent +
- value, property +
- lattice – coordinate system for fractional coordinates, +
- an instance of Lattice or None for Cartesian system +
+- Private data: +
_U – storage of U property, 3x3 numpy matrix +_Uisoequiv – storage of Uisoequiv property, float +_anisotropy – storage of anisotropy property, bool or
++
+None when not determined-
+
- _Usynced – flag for consistency of _U with _Uisoequiv, +
- it is meaningful only for isotropic atoms +
+- Class data: +
- tol_anisotropy – tolerated U matrix deviation for isotropic atom +
-
+
- +B11¶ +
B11 element of Debye-Waler displacement tensor
+
-
+
- +B12¶ +
B12 element of Debye-Waler displacement tensor
+
-
+
- +B13¶ +
B13 element of Debye-Waler displacement tensor
+
-
+
- +B22¶ +
B22 element of Debye-Waler displacement tensor
+
-
+
- +B23¶ +
B23 element of Debye-Waler displacement tensor
+
-
+
- +B33¶ +
B33 element of Debye-Waler displacement tensor
+
-
+
- +Bisoequiv¶ +
Debye-Waler isotropic thermal displacement or equivalent value
+
-
+
- +U¶ +
anisotropic thermal displacement tensor.
+
-
+
- +U11¶ +
U11 element of anisotropic displacement tensor
+
-
+
- +U12¶ +
U12 element of anisotropic displacement tensor
+
-
+
- +U13¶ +
U13 element of anisotropic displacement tensor
+
-
+
- +U22¶ +
U22 element of anisotropic displacement tensor
+
-
+
- +U23¶ +
U23 element of anisotropic displacement tensor
+
-
+
- +U33¶ +
U33 element of anisotropic displacement tensor
+
-
+
- +Uisoequiv¶ +
isotropic thermal displacement or equivalent value
+
-
+
- +anisotropy¶ +
flag for anisotropic thermal displacements.
+
-
+
- +element = ''¶ +
-
+
- +label = ''¶ +
-
+
- +lattice = None¶ +
-
+
- +msdCart(vc)¶ +
mean square displacement of an atom along cartesian vector
+vc – vector in absolute cartesian coordinates
+return mean square displacement
+
-
+
- +msdLat(vl)¶ +
mean square displacement of an atom along lattice vector
+vl – vector in lattice coordinates
+return mean square displacement
+
-
+
- +occupancy = 1.0¶ +
-
+
- +tol_anisotropy = 1e-06¶ +
-
+
- +x¶ +
fractional coordinate x.
+
-
+
- +xyz_cartn¶ +
absolute Cartesian coordinates of an atom
+
-
+
- +y¶ +
fractional coordinate y.
+
-
+
- +z¶ +
fractional coordinate z.
+
+
+bratomsstructure Module¶
+definition of BRAtomsStructure class derived from Structure
+-
+
- +class diffpy.Structure.bratomsstructure.BRAtomsStructure(*args, **kwargs)¶ +
Bases: diffpy.Structure.structure.Structure
+-
+
- BRAtomsStructure –> Structure with extra information for use with Bruce +
Ravel’s atoms program.
+-
+
- Data members: +
-
+
- bratoms – dictionary for storing following extra parameters from +
- atoms .inp files. +‘space’, ‘output’, ‘rmax’, ‘core’, ‘edge’, ‘shift’, +‘nitrogen’, ‘argon’, ‘krypton’ +
see the following web site for descriptions.
+
+
+
http://leonardo.phys.washington.edu/~ravel/software/doc/Atoms/Atoms/node7.html
+
+
+lattice Module¶
+class Lattice stores properites and provides simple operations in lattice +coordinate system.
+-
+
- Module variables: +
- cartesian – constant instance of Lattice, default Cartesian system +
-
+
- +class diffpy.Structure.lattice.Lattice(a=None, b=None, c=None, alpha=None, beta=None, gamma=None, baserot=None, base=None)¶ +
Bases: object
+Lattice –> general coordinate system
+Data members:
++
+-
+
- a, b, c, alpha, beta, gamma – lattice parameters with cell angles +
- in degrees, read-write properties. Assignment to cell +parameters calls the setLatPar method. The lattice parameters +can be also changed by calling the setLatBase method. +
- ar, br, cr, alphar, betar, gammar – cell parameters for the +
- reciprocal lattice. Their values reflect the direct cell +parameters and the calls to setLatPar or setLatBase methods. +The reciprocal angles are in degrees. Read-only properties. +
- ca, cb, cg, sa, sb, sg – cosines and sines of the lattice angles, +
- read-only properties +
- car, cbr, cgr, sar, sbr, sgr – cosines and sines of the reciprocal +
- lattice angles, read-only properties. +
metrics – metrics tensor +base – matrix of row base vectors in Cartesian coordinates,
++
+base = stdbase*baserotstdbase – matrix of base vectors in standard orientation +baserot – base rotation matrix +recbase – inverse of base matrix, its columns are reciprocal
++
+vectors in Cartesian coordinatesnormbase – base with magnitudes of reciprocal vectors +recnormbase – inverse of normbase
+Note: All data members except a, b, c, alpha, beta, gamma are read-only. +Their values get updated by setting the lattice parameters or calling +the setLatPar() or setLatBase() methods.
+-
+
- +a¶ +
Unit cell length a
+
-
+
- +abcABG()¶ +
Return a tuple of 6 lattice parameters.
+
-
+
- +alpha¶ +
Cell angle alpha in degrees
+
-
+
- +alphar¶ +
Reciprocal lattice angle alpha in degrees
+
-
+
- +angle(u, v)¶ +
Return angle(u, v) –> angle of 2 lattice vectors in degrees.
+
-
+
- +ar¶ +
Cell length a of the reciprocal lattice
+
-
+
- +b¶ +
Unit cell length b
+
-
+
- +beta¶ +
Cell angle beta in degrees
+
-
+
- +betar¶ +
Reciprocal lattice angle beta in degrees
+
-
+
- +br¶ +
Cell length b of the reciprocal lattice
+
-
+
- +c¶ +
Unit cell length c
+
-
+
- +ca¶ +
Cosine of the cell angle alpha
+
-
+
- +car¶ +
Cosine of the reciprocal angle alpha
+
-
+
- +cartesian(u)¶ +
Return Cartesian coordinates of a lattice vector.
+
-
+
- +cb¶ +
Cosine of the cell angle beta
+
-
+
- +cbr¶ +
Cosine of the reciprocal angle beta
+
-
+
- +cg¶ +
Cosine of the cell angle gamma
+
-
+
- +cgr¶ +
Cosine of the reciprocal angle gamma
+
-
+
- +cr¶ +
Cell length c of the reciprocal lattice
+
-
+
- +dist(u, v)¶ +
Return distance of 2 points in lattice coordinates.
+
-
+
- +dot(u, v)¶ +
Return dot product of 2 lattice vectors.
+
-
+
- +fractional(rc)¶ +
Return fractional coordinates of a Cartesian vector.
+
-
+
- +gamma¶ +
Cell angle gamma in degrees
+
-
+
- +gammar¶ +
Reciprocal lattice angle gamma in degrees
+
-
+
- +norm(u)¶ +
Return norm of the specified lattice vector.
+
-
+
- +reciprocal()¶ +
Return the reciprocal lattice to self.
+
-
+
- +sa¶ +
Sine of the cell angle alpha
+
-
+
- +sar¶ +
Sine of the reciprocal angle alpha
+
-
+
- +sb¶ +
Sine of the cell angle beta
+
-
+
- +sbr¶ +
Sine of the reciprocal angle beta
+
-
+
- +setLatBase(base)¶ +
Set matrix of unit cell base vectors and calculate corresponding +lattice parameters and stdbase, baserot and metrics tensors.
+No return value.
+
-
+
- +setLatPar(a=None, b=None, c=None, alpha=None, beta=None, gamma=None, baserot=None)¶ +
set lattice parameters and all related tensors
+-
+
- a, b, c, alpha, beta, gamma – lattice parameters, unit cell angles +
- are in degrees. +
baserot – unit cell rotation, base = stdbase*baserot
+Note: parameters with value None will remain unchanged.
+No return value.
+
-
+
- +sg¶ +
Sine of the cell angle gamma
+
-
+
- +sgr¶ +
Sine of the reciprocal angle gamma
+
-
+
- +unitvolume¶ +
Cell volume assuming a=b=c=1
+
-
+
- +volume¶ +
Lattice cell volume
+
-
+
- +diffpy.Structure.lattice.cosd(x)¶ +
Return the cosine of x (measured in degrees). +Avoid round-off errors for exact cosine values.
+
-
+
- +diffpy.Structure.lattice.sind(x)¶ +
Return the sine of x (measured in degrees). +Avoid round-off errors for exact sine values.
+
+
+mmlibspacegroups Module¶
+Space groups defined as a part of the pymmlib.
+
+
+pdffitstructure Module¶
+definition of PDFFitStructure class derived from Structure
+-
+
- +class diffpy.Structure.pdffitstructure.PDFFitStructure(*args, **kwargs)¶ +
Bases: diffpy.Structure.structure.Structure
+PDFFitStructure –> Structure with extra pdffit member
+-
+
- Data members: +
-
+
- pdffit – dictionary for storing following extra parameters from +
-
+
- PDFFit structure files: +
- ‘scale’, ‘delta1’, ‘delta2’, ‘sratio’, +‘rcut’, ‘spcgr’, ‘dcell’, ‘ncell’ +
+
+
-
+
- +read(filename, format='auto')¶ +
Same as Structure.read, but update spcgr value in +self.pdffit when parser can get spacegroup.
+Return instance of StructureParser used to load the data. +See Structure.read() for more info.
+
-
+
- +readStr(s, format='auto')¶ +
Same as Structure.readStr, but update spcgr value in +self.pdffit when parser can get spacegroup.
+Return instance of StructureParser used to load the data. +See Structure.readStr() for more info.
+
+
+sgtbxspacegroups Module¶
+Extra space group representations generated using sgtbx module from cctbx. +Import of this module extends the SpaceGroupList in the SpaceGroups module. +Notable variables:
+sgtbxSpaceGroupList – list of space group instances defined in this module
+
+
+spacegroupmod Module¶
+Symmetry operations as functions on vectors or arrays.
+-
+
- +class diffpy.Structure.spacegroupmod.SpaceGroup(number=None, num_sym_equiv=None, num_primitive_sym_equiv=None, short_name=None, alt_name=None, point_group_name=None, crystal_system=None, pdb_name=None, symop_list=None)¶ +
Bases: object
+Contains the various names and symmetry operations for one space +group.
+-
+
- +check_group_name(name)¶ +
Checks if the given name is a name for this space group, +returns True or False. The space group name can be in several forms: +the short name, the longer PDB-style name, or the space group number.
+
-
+
- +iter_equivalent_positions(vec)¶ +
Iterate the symmetry equivelant positions of the argument vector. +The vector must already be in fractional coordinates, and the +symmetry equivelant vectors are also in fractional coordinates.
+
-
+
- +iter_symops()¶ +
Iterates over all SymOps in the SpaceGroup.
+
+
+structure Module¶
+This module defines class Structure.
+-
+
- +class diffpy.Structure.structure.Structure(atoms=[], lattice=None, title=None, filename=None, format=None)¶ +
Bases: list
+Structure –> group of atoms
+Structure class is inherited from Python list. It contains +a list of Atom instances. Structure overloads setitem and setslice +methods so that the lattice attribute of atoms get set to lattice.
+-
+
- Data members: +
- title – structure description +lattice – coordinate system (instance of Lattice) +pdffit – None or a dictionary of PDFFit-related metadata +
-
+
- +B11¶ +
Array of B11 elements of the Debye-Waller displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +B12¶ +
Array of B12 elements of the Debye-Waller displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +B13¶ +
Array of B13 elements of the Debye-Waller displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +B22¶ +
Array of B22 elements of the Debye-Waller displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +B23¶ +
Array of B23 elements of the Debye-Waller displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +B33¶ +
Array of B33 elements of the Debye-Waller displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +Bisoequiv¶ +
Array of Debye-Waller isotropic thermal displacement or equivalent +values. Assignment updates the U attribute of all atoms.
+
-
+
- +U¶ +
Array of anisotropic thermal displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +U11¶ +
Array of U11 elements of the anisotropic displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +U12¶ +
Array of U12 elements of the anisotropic displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +U13¶ +
Array of U13 elements of the anisotropic displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +U22¶ +
Array of U22 elements of the anisotropic displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +U23¶ +
Array of U23 elements of the anisotropic displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +U33¶ +
Array of U33 elements of the anisotropic displacement tensors. +Assignment updates the U and anisotropy attributes of all atoms.
+
-
+
- +Uisoequiv¶ +
Array of isotropic thermal displacement or equivalent values. +Assignment updates the U attribute of all atoms.
+
-
+
- +addNewAtom(*args, **kwargs)¶ +
Add new Atom instance to the end of this Structure.
+All arguments are forwarded to Atom constructor.
+No return value.
+
-
+
- +angle(aid0, aid1, aid2)¶ +
The bond angle at the second of three atoms in degrees.
+-
+
- aid0 – zero based index of the first atom or a string label +
- such as “Na1” +
- aid1 – index or string label for the second atom, +
- where the angle is formed +
aid2 – index or string label for the third atom
+Return float. +Raise IndexError for invalid arguments.
+
-
+
- +anisotropy¶ +
Boolean array for anisotropic thermal displacement flags. +Assignment updates the anisotropy attribute of all atoms.
+
-
+
- +append(a, copy=True)¶ +
Append atom to a structure and update its lattice attribute.
+a – instance of Atom +copy – flag for appending a copy of a.
++
+When False, append a and update a.lattice.No return value.
+
-
+
- +assignUniqueLabels()¶ +
Set a unique label string for each atom in this structure. +The label strings are formatted as “%(baresymbol)s%(index)i”, +where baresymbol is the element right-stripped of “[0-9][+-]”.
+No return value.
+
-
+
- +composition¶ +
Dictionary of chemical symbols and their total occupancies.
+
-
+
- +distance(aid0, aid1)¶ +
Distance between 2 atoms, no periodic boundary conditions.
+-
+
- aid0 – zero based index of the first atom or a string label +
- such as “Na1” +
aid1 – zero based index or string label of the second atom.
+Return float. +Raise IndexError for invalid arguments.
+
-
+
- +element¶ +
Character array of atom types. Assignment updates +the element attribute of the respective atoms.
+
-
+
- +extend(atoms, copy=True)¶ +
Extend Structure by appending copies from a list of atoms.
+atoms – list of Atom instances +copy – flag for extending with copies of Atom instances.
++
+When False extend with atoms and update their lattice +attributes.No return value.
+
-
+
- +getLastAtom()¶ +
Return Reference to the last Atom in this structure.
+
-
+
- +insert(idx, a, copy=True)¶ +
Insert atom a before position idx in this Structure.
+idx – position in atom list +a – instance of Atom +copy – flag for inserting a copy of a.
++
+When False, append a and update a.lattice.No return value.
+
-
+
- +label¶ +
Character array of atom names. Assignment updates +the label attribute of all atoms.
+
-
+
- +lattice¶ +
Coordinate system for this Structure.
+
-
+
- +occupancy¶ +
Array of atom occupancies. Assignment updates the +occupancy attribute of all atoms.
+
-
+
- +pdffit = None¶ +
-
+
- +placeInLattice(new_lattice)¶ +
place structure into new_lattice coordinate system
+sets lattice to new_lattice and recalculate fractional coordinates +of all atoms so their absolute positions remain the same
+return self
+
-
+
- +read(filename, format='auto')¶ +
Load structure from a file, any original data become lost.
+filename – file to be loaded +format – all structure formats are defined in Parsers submodule,
++
+when format == ‘auto’ all Parsers are tried one by oneReturn instance of data Parser used to process file. This +can be inspected for information related to particular format.
+
-
+
- +readStr(s, format='auto')¶ +
Load structure from a string, any original data become lost.
+s – string with structure definition +format – all structure formats are defined in Parsers submodule,
++
+when format == ‘auto’ all Parsers are tried one by oneReturn instance of data Parser used to process input string. This +can be inspected for information related to particular format.
+
-
+
- +title = ''¶ +
-
+
- +tolist()¶ +
Return atoms in this Structure as a standard Python list.
+
-
+
- +write(filename, format)¶ +
Save structure to file in the specified format
+No return value.
+-
+
- Note: available structure formats can be obtained by: +
- from Parsers import formats +
-
+
- +writeStr(format)¶ +
return string representation of the structure in specified format
+-
+
- Note: available structure formats can be obtained by: +
- from Parsers import formats +
-
+
- +x¶ +
Array of all fractional coordinates x. +Assignment updates xyz attribute of all atoms.
+
-
+
- +xyz¶ +
Array of fractional coordinates of all atoms. +Assignment updates xyz attribute of all atoms.
+
-
+
- +xyz_cartn¶ +
Array of absolute Cartesian coordinates of all atoms. +Assignment updates the xyz attribute of all atoms.
+
-
+
- +y¶ +
Array of all fractional coordinates y. +Assignment updates xyz attribute of all atoms.
+
-
+
- +z¶ +
Array of all fractional coordinates z. +Assignment updates xyz attribute of all atoms.
+
+
+utils Module¶
+Small shared functions.
+-
+
- +diffpy.Structure.utils.atomBareSymbol(smbl)¶ +
Remove atom type string stripped of isotope and ion charge symbols. +This removes blank and leading [0-9-] or trailing [1-9][+-] characters.
+smbl – atom type string such as “Cl-”, “Ca2+” or “12-C”.
+Return bare element symbol.
+
-
+
- +diffpy.Structure.utils.isfloat(s)¶ +
True if argument can be converted to float
+
+
+version Module¶
+Definition of __version__, __date__, __gitsha__.
+
+
+Subpackages¶
+
+
+-
+
- Parsers Package + +
- applications Package + +
- expansion Package + +
- tests Package + +
+
+
+
+
+
\ No newline at end of file
diff --git a/api/diffpy.html b/api/diffpy.html
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index 00000000..0ffadd02
--- /dev/null
+++ b/api/diffpy.html
@@ -0,0 +1,167 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ tests Package¶
+
+
+tests Package¶
+Unit tests for diffpy.Structure.
+-
+
- +diffpy.Structure.tests.test()¶ +
Execute all unit tests for the diffpy.Structure package. +Return a unittest TestResult object.
+
-
+
- +diffpy.Structure.tests.testsuite()¶ +
Build a unit tests suite for the diffpy.Structure package.
+Return a unittest.TestSuite object.
+
+
+TestLattice Module¶
+Unit tests for Lattice class.
+-
+
- +class diffpy.Structure.tests.TestLattice.TestLattice(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test methods of Lattice class
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +setUp()¶ +
-
+
- +test_latpar_properties()¶ +
check assignment to a, b, c, alpha, beta, gamma.
+
-
+
- +test_readonly_properties()¶ +
Check that read-only properties are indeed such.
+
-
+
- +test_repr()¶ +
check string representation of this lattice
+
-
+
- +test_setLatBase()¶ +
check calculation of unit cell rotation
+
-
+
- +test_setLatPar()¶ +
check calculation of standard unit cell vectors
+
+
+TestLoadStructure Module¶
+Unit tests for the loadStructure factory.
+-
+
- +class diffpy.Structure.tests.TestLoadStructure.TestLoadStructure(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+-
+
- +test_badfile()¶ +
check loading of CIF file format
+
-
+
- +test_cif()¶ +
check loading of CIF file format
+
-
+
- +test_discus()¶ +
check loading of discus file format
+
-
+
- +test_xcfg()¶ +
check loading of atomeye xcfg format
+
+
+TestP_cif Module¶
+Unit tests for diffpy.Structure.Parsers.P_cif module
+-
+
- +class diffpy.Structure.tests.TestP_cif.TestP_cif(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +badciffile = '/home/juhas/programs/github/diffpy/diffpy.Structure/diffpy/Structure/tests/testdata/LiCl-bad.cif'¶ +
-
+
- +cdsebulkpdffitfile = '/home/juhas/programs/github/diffpy/diffpy.Structure/diffpy/Structure/tests/testdata/CdSe_bulk.stru'¶ +
-
+
- +goodciffile = '/home/juhas/programs/github/diffpy/diffpy.Structure/diffpy/Structure/tests/testdata/PbTe.cif'¶ +
-
+
- +graphiteciffile = '/home/juhas/programs/github/diffpy/diffpy.Structure/diffpy/Structure/tests/testdata/graphite.cif'¶ +
-
+
- +places = 6¶ +
-
+
- +setUp()¶ +
-
+
- +tearDown()¶ +
-
+
- +teiciffile = '/home/juhas/programs/github/diffpy/diffpy.Structure/diffpy/Structure/tests/testdata/TeI.cif'¶ +
-
+
- +test_parse()¶ +
check P_cif.parse()
+
-
+
- +test_parseFile()¶ +
check P_cif.parseFile()
+
-
+
- +test_parseLines()¶ +
check P_cif.parseLines()
+
-
+
- +test_write_and_read()¶ +
high-level check of P_cif.tostring()
+
+
+TestP_discus Module¶
+Unit tests for diffpy.Structure.Parsers.P_discus module
+-
+
- +class diffpy.Structure.tests.TestP_discus.TestP_discus(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for PDFFit file format
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +setUp()¶ +
-
+
- +test_except_other_formats()¶ +
check exceptions when reading files in other formats
+
-
+
- +test_ignored_lines()¶ +
check skipping of ignored lines in the header
+
-
+
- +test_read_discus_Ni()¶ +
check reading of Ni structure in discus format
+
-
+
- +test_spdiameter_parsing()¶ +
check parsing of spdiameter record from a file.
+
-
+
- +test_stepcut_parsing()¶ +
check parsing of stepcut record from a file.
+
-
+
- +diffpy.Structure.tests.TestP_discus.assertListAlmostEqual(self, l1, l2, places=None)¶ +
wrapper for list comparison
+
+
+TestP_pdffit Module¶
+Unit tests for diffpy.Structure.Parsers.P_pdffit module
+-
+
- +class diffpy.Structure.tests.TestP_pdffit.TestP_pdffit(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for PDFFit file format
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +setUp()¶ +
-
+
- +test_huge_occupancy()¶ +
check structure with huge occupancy can be read.
+
-
+
- +test_ignored_lines()¶ +
check skipping of ignored lines in the header
+
-
+
- +test_read_pdffit_Ni()¶ +
check reading of Ni pdffit structure file
+
-
+
- +test_read_pdffit_Ni_prim123()¶ +
check reading of Ni_prim supercell 1x2x3
+
-
+
- +test_read_pdffit_ZnSb()¶ +
check reading of ZnSb pdffit structure file
+
-
+
- +test_read_pdffit_bad()¶ +
check exceptions when reading invalid pdffit file
+
-
+
- +test_spdiameter_parsing()¶ +
check parsing of spdiameter record from a file.
+
-
+
- +test_stepcut_parsing()¶ +
check parsing of stepcut record from a file.
+
-
+
- +test_writeStr_pdffit()¶ +
check writing of normal xyz file
+
-
+
- +diffpy.Structure.tests.TestP_pdffit.assertListAlmostEqual(self, l1, l2, places=None)¶ +
wrapper for list comparison
+
+
+TestParsers Module¶
+Unit tests for Structure.Parsers module.
+-
+
- +class diffpy.Structure.tests.TestParsers.TestP_bratoms(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for Bruce Ravel’s atoms file format
+-
+
- +setUp()¶ +
-
+
- +test_read_bratoms_bad()¶ +
check exceptions when reading invalid bratoms file
+
-
+
- +test_writeStr_cif()¶ +
check conversion to CIF string
+
-
+
- +class diffpy.Structure.tests.TestParsers.TestP_pdb(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for PDB file format
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +setUp()¶ +
-
+
- +test_read_pdb_arginine()¶ +
check reading of arginine PDB file
+
-
+
- +test_rwStr_pdb_CdSe()¶ +
check conversion to PDB file format
+
-
+
- +class diffpy.Structure.tests.TestParsers.TestP_rawxyz(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for rawxyz file format
+-
+
- +setUp()¶ +
-
+
- +test_read_plainxyz()¶ +
check reading of a plain xyz file
+
-
+
- +test_read_plainxyz_bad()¶ +
check exceptions when reading invalid plain xyz file
+
-
+
- +test_read_rawxyz()¶ +
check reading of raw xyz file
+
-
+
- +test_read_rawxyz_bad()¶ +
check exceptions when reading unsupported xy file
+
-
+
- +test_writeStr_rawxyz()¶ +
check writing of normal xyz file
+
-
+
- +class diffpy.Structure.tests.TestParsers.TestP_xcfg(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for XCFG file format
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +setUp()¶ +
-
+
- +test_read_xcfg()¶ +
check reading of BubbleRaft XCFG file
+
-
+
- +test_rwStr_xcfg_CdSe()¶ +
check conversion to XCFG file format
+
-
+
- +class diffpy.Structure.tests.TestParsers.TestP_xyz(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test Parser for xyz file format
+-
+
- +setUp()¶ +
-
+
- +tearDown()¶ +
-
+
- +test_read_xyz()¶ +
check reading of normal xyz file
+
-
+
- +test_read_xyz_bad()¶ +
check exceptions when reading invalid xyz file
+
-
+
- +test_writeStr_xyz()¶ +
check string representation of normal xyz file
+
-
+
- +test_write_xyz()¶ +
check writing of normal xyz file
+
-
+
- +diffpy.Structure.tests.TestParsers.assertListAlmostEqual(self, l1, l2, places=None)¶ +
wrapper for list comparison
+
+
+TestStructure Module¶
+Unit tests for Structure class.
+-
+
- +class diffpy.Structure.tests.TestStructure.TestStructure(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+test methods of Structure class
+-
+
- +assertListAlmostEqual(l1, l2, places=None)¶ +
wrapper for list comparison
+
-
+
- +setUp()¶ +
-
+
- +test_Bij()¶ +
check Structure.Bij
+
-
+
- +test_Bisoequiv()¶ +
check Structure.Bisoequiv
+
-
+
- +test_U()¶ +
check Structure.U
+
-
+
- +test_Uij()¶ +
check Structure.Uij
+
-
+
- +test_Uisoequiv()¶ +
check Structure.Uisoequiv
+
-
+
- +test___add__()¶ +
check Structure.__add__()
+
-
+
- +test___copy__()¶ +
check Structure.__copy__()
+
-
+
- +test___getitem__()¶ +
check Structure.__getitem__()
+
-
+
- +test___getslice__()¶ +
check Structure.__getslice__()
+
-
+
- +test___iadd__()¶ +
check Structure.__iadd__()
+
-
+
- +test___imul__()¶ +
check Structure.__imul__()
+
-
+
- +test___isub__()¶ +
check Structure.__isub__()
+
-
+
- +test___mul__()¶ +
check Structure.__mul__()
+
-
+
- +test___setitem__()¶ +
check Structure.__setitem__()
+
-
+
- +test___setslice__()¶ +
check Structure.__setslice__()
+
-
+
- +test___sub__()¶ +
check Structure.__sub__()
+
-
+
- +test__get_lattice()¶ +
check Structure._get_lattice()
+
-
+
- +test__set_lattice()¶ +
check Structure._set_lattice()
+
-
+
- +test_angle()¶ +
check Structure.angle()
+
-
+
- +test_anisotropy()¶ +
check Structure.anisotropy
+
-
+
- +test_append()¶ +
check Structure.append()
+
-
+
- +test_aslist()¶ +
check Structure.tolist()
+
-
+
- +test_assignUniqueLabels()¶ +
check Structure.assignUniqueLabels()
+
-
+
- +test_cartesian()¶ +
check conversion to cartesian coordinates
+
-
+
- +test_distance()¶ +
check Structure.distance()
+
-
+
- +test_element()¶ +
check Structure.element
+
-
+
- +test_extend()¶ +
check Structure.extend()
+
-
+
- +test_insert()¶ +
check Structure.insert()
+
-
+
- +test_label()¶ +
check Structure.label
+
-
+
- +test_occupancy()¶ +
check Structure.occupancy
+
-
+
- +test_placeInLattice()¶ +
check Structure.placeInLattice() – conversion of coordinates
+
-
+
- +test_x()¶ +
check Structure.x
+
-
+
- +test_xyz()¶ +
check Structure.xyz
+
-
+
- +test_xyz_cartn()¶ +
check Structure.xyz_cartn
+
-
+
- +test_y()¶ +
check Structure.y
+
-
+
- +test_z()¶ +
check Structure.z
+
+
+TestSuperCell Module¶
+Unit tests for supercell.py
+-
+
- +class diffpy.Structure.tests.TestSuperCell.TestSuperCell(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+-
+
- +setUp()¶ +
-
+
- +stru_cdse = None¶ +
-
+
- +stru_ni = None¶ +
-
+
- +tearDown()¶ +
-
+
- +test_cdse_supercell()¶ +
check supercell expansion for CdSe.
+
-
+
- +test_exceptions()¶ +
check argument checking of supercell.
+
-
+
- +test_ni_supercell()¶ +
check supercell expansion for Ni.
+
+
+TestSymmetryUtilities Module¶
+Unit tests for SymmetryUtilities.py
+-
+
- +class diffpy.Structure.tests.TestSymmetryUtilities.TestGeneratorSite(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+-
+
- +generators = {}¶ +
-
+
- +setUp()¶ +
-
+
- +tearDown()¶ +
-
+
- +test_UFormula()¶ +
check GeneratorSite.UFormula()
+
-
+
- +test_UFormula_g186c_eqxyz()¶ +
Check rotated U formulas at the symmetry positions of c-site in 186.
+
-
+
- +test___init__()¶ +
check GeneratorSite.__init__()
+
-
+
- +test__findUParameters()¶ +
check GeneratorSite._findUParameters()
+
-
+
- +test_eqIndex()¶ +
check GeneratorSite.eqIndex()
+
-
+
- +test_positionFormula()¶ +
check GeneratorSite.positionFormula()
+
-
+
- +class diffpy.Structure.tests.TestSymmetryUtilities.TestRoutines(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+-
+
- +setUp()¶ +
-
+
- +tearDown()¶ +
-
+
- +test_expandPosition()¶ +
check expandPosition()
+
-
+
- +test_isSpaceGroupLatPar()¶ +
check isSpaceGroupLatPar()
+
-
+
- +test_isconstantFormula()¶ +
check isconstantFormula()
+
-
+
- +test_pruneFormulaDictionary()¶ +
check pruneFormulaDictionary()
+
-
+
- +class diffpy.Structure.tests.TestSymmetryUtilities.TestSymmetryConstraints(methodName='runTest')¶ +
Bases: unittest.case.TestCase
+-
+
- +setUp()¶ +
-
+
- +tearDown()¶ +
-
+
- +test_UparSymbols()¶ +
check SymmetryConstraints.UparSymbols()
+
-
+
- +test_UparValues()¶ +
check SymmetryConstraints.UparValues()
+
-
+
- +test___init__()¶ +
check SymmetryConstraints.__init__()
+
-
+
- +test_corepos()¶ +
test_corepos - find positions in the asymmetric unit.
+
+
+
+run Module¶
+Convenience module for executing all unit tests with
+python -m diffpy.Structure.tests.run
+
+
+
+
+
+
\ No newline at end of file
diff --git a/api/modules.html b/api/modules.html
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--- /dev/null
+++ b/api/modules.html
@@ -0,0 +1,130 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ diffpy API¶
+
+
+-
+
- Structure Package
-
+
- Structure Package +
- SpaceGroups Module +
- StructureErrors Module +
- SymmetryUtilities Module +
- atom Module +
- bratomsstructure Module +
- lattice Module +
- mmlibspacegroups Module +
- pdffitstructure Module +
- sgtbxspacegroups Module +
- spacegroupmod Module +
- structure Module +
- utils Module +
- version Module +
- Subpackages
-
+
- Parsers Package + +
- applications Package + +
- expansion Package + +
- tests Package + +
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/genindex.html b/genindex.html
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+ diffpy¶
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+-
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- diffpy API
-
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- Structure Package
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+
- Structure Package +
- SpaceGroups Module +
- StructureErrors Module +
- SymmetryUtilities Module +
- atom Module +
- bratomsstructure Module +
- lattice Module +
- mmlibspacegroups Module +
- pdffitstructure Module +
- sgtbxspacegroups Module +
- spacegroupmod Module +
- structure Module +
- utils Module +
- version Module +
- Subpackages + +
+
+ - Structure Package
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-Placeholder for documentation for diffpy.Structure
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+ Index
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+ A
+ | B
+ | C
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+ Welcome to Structure documentation!¶
+diffpy.Structure - simple storage and manipulation of crystal structures
+Contents:
+
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+
- Introduction + +
- Installation + +
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+ Installation¶
+
+
+Requirements¶
+The diffpy.Structure requires Python 2.5 and the following external software:
+++setuptools – software distribution tools for Python +numpy – numerical mathematics and fast array operations for Python
On Ubuntu Linux the required software can be easily installed using +the system package manager:
++++
+- sudo aptitude install
+- python-setuptools python-numpy
+
For other Linux distributions use their respective package manager; note +the packages may have slightly different names. diffpy.Structure should work +on other Unix-like operating systems and on Mac as well. Please, search the +web for instructions how to install external dependencies on your particular +system.
+
+
+Installation¶
+To install the diffpy.Structure package:
+++python setup.py install
By default the files are installed in the system directories, which are +usually only writeable by the root. See the usage info +”./setup.py install –help” for options to install as a normal user under +different location. Note that installation to non-standard directories may +require adjustments to the PATH and PYTHONPATH environment variables.
+The Python setuptools library provides “easy_install” script, which can +be used to update diffpy.Structure installation or even to perform a new +install without explicit need to download and unzip the code:
+++easy_install -U diffpy.Structure
This checks the package repository at http://www.diffpy.org/packages/ +for any newer releases of diffpy.Structure and if present, it updates the +installation.
+
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+
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diff --git a/objects.inv b/objects.inv
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index 0000000000000000000000000000000000000000..66961e0d0e1e0be6aa897a8de25fb1e79948e60c
GIT binary patch
literal 3924
zcmV-a53BGaAX9K?X>NERX>N99Zgg*Qc_4OWa&u{KZXhxWBOp+6Z)#;@bUGkYbaHiL
zbairN3L_v^WpZ
+
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+
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+ Introduction¶
+diffpy.Structure - simple storage and manipulation of crystal structures
+The diffpy.Structure package provides simple crystal structure operation +such as calculations of distances or angles from fractional coordinates. +It also provides imports and exports in several structure file formats +and space group definitions and utilities for symmetry expansion and +generation of symmetry constraints on positions and thermal factors.
+To learn more about diffpy.Structure library, see the examples directory +included in this distribution or the API documentation at
+++
+
+License notice¶
+This program is part of the DiffPy and DANSE open-source projects +and is available subject to the conditions and terms laid out below.
+If you use this program to do productive scientific research that leads +to publication, we ask that you acknowledge use of the program by citing +the following paper in your publication:
+++P. Juhas, C. L. Farrow, J. W. Liu, D. Bryndin, E. S. Bozin, +W. Zhou and S. J. L. Billinge, DiffPy library - Python packages +for diffraction analysis. To be published.
Copyright 2006-2007, Board of Trustees of Michigan State University, +Copyright 2008-2009, Board of Trustees of Columbia University in the +city of New York. (Copyright holder indicated in each source file).
+-
+
- For more information please visit the project web-page: +
- http://www.diffpy.org/ +
or email Prof. Simon Billinge at sb2896@columbia.edu
+Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met:
++++
+- Redistributions of source code must retain the above copyright +notice, this list of conditions and the following disclaimer.
+- Redistributions in binary form must reproduce the above copyright +notice, this list of conditions and the following disclaimer in the +documentation and/or other materials provided with the distribution.
+- Neither the name of the copyright holder nor the names of its +contributors may be used to endorse or promote products derived from +this software without specific prior written permission.
+
THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER “AS IS”. COPYRIGHT HOLDER +EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER +EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY +FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM +INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE +SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY. IN NO EVENT SHALL +COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR ANY DIRECT, INDIRECT, +INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT +NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF +USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF +THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE.
+
+
+Authors¶
+This code was developed as part of the DiffPy project to create python +modules for structure investigations from diffraction data. The main +contributors to this package were
+++Pavol Juhas +Chris Farrow
The DiffPy team is located in the Billinge-group at the Applied Physics +and Applied Mathematics Department of the Columbia University in New York. +Currently the team consists of
+++Simon Billinge +Pavol Juhas +Chris Farrow +Jiwu Liu +Yingrui Shang +Emil Bozin +Peng Tian
Please see the header of each source file for a detailed list of +contributors. This is an open-source project and we hope and expect +that the list of contributors will expand with time. Many thanks to +all current and future contributors!
+For more information on the DiffPy project email sb2896@columbia.edu
+DiffPy was initiated as part of the Distributed Data Analysis of Neutron +Scattering Experiments (DANSE) project, funded by the National Science +Foundation under grant DMR-0520547. More information on DANSE can be +found at http://danse.us. Any opinions, findings, and conclusions or +recommendations expressed in this material are those of the author(s) +and do not necessarily reflect the views of the NSF.
+Acknowledgments:
+We are truly grateful to all the people who have contributed, in all +different ways, to this project: Thomas Proffen, Xiangyun Qiu, Pete +Peterson and Jacques Bloch, previous Billinge-group members whose +contributions to the codes are living well beyond their affiliation with +the group; The hard working DANSE group at Caltech, University of +Maryland, Iowa State and University of Tennessee, especially Brent Fultz +for doggedly putting DANSE all together and Michael Aivazis, and the +indomitable Mike McKerns for their design input and MM’s gargantuan +excel spreadsheets; The former members of the Billinge-group members, +especially HyunJeong Kim and Ahmad Masadeh for enthusiastic testing and +feature requests; Last but not least, our long suffering family members, +and the whole coffee and tea industries at large, without whom none of +this would have been possible.
+Last modified $Date$
+
+
+
+
+
+
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+ Python Module Index
+ + + +
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\ No newline at end of file
From ab69b8b33434443e6f73bfedf4990bd958bd49ca Mon Sep 17 00:00:00 2001
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