Changeset 4306


Ignore:
Timestamp:
Feb 15, 2020 10:04:50 AM (21 months ago)
Author:
vondreele
Message:

major doc edits

File:
1 edited

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  • trunk/GSASIIobj.py

    r4303 r4306  
    158158==========  ===============  ====================================================
    159159General         \            Overall information for the phase (dict)
    160   \         AtomPtrs         list of four locations to use to pull info
     160  \         3Dproj           projections for 3D pole distribution plots
     161  \         AngleRadii       Default radius for each atom used to compute
     162                             interatomic angles (list of floats)
     163  \         AtomMass         List of masses for atoms
     164  \         AtomPtrs         list of four locations (cx,ct,cs & cu) to use to pull info
    161165                             from the atom records (list)
    162   \         F000X            x-ray F(000) intensity (float)
    163   \         F000N            neutron F(000) intensity (float)
    164   \         Mydir            directory of current .gpx file (str)
    165   \         MCSA controls    Monte Carlo-Simulated Annealing controls (dict)
     166  \         AtomTypes        List of atom types
     167  \         BondRadii        Default radius for each atom used to compute
     168                             interatomic distances (list of floats)
    166169  \         Cell             List with 8 items: cell refinement flag (bool)
    167170                             a, b, c, (Angstrom, float)
    168171                             alpha, beta & gamma (degrees, float)
    169172                             volume (A^3, float)
    170   \         Type             'nuclear' or 'macromolecular' for now (str)
    171   \         Map              dict of map parameters
    172   \         SH Texture       dict of spherical harmonic preferred orientation
    173                              parameters
    174   \         Isotope          dict of isotopes for each atom type
    175   \         Isotopes         dict of scattering lengths for each isotope
    176                              combination for each element in phase
    177   \         Name             phase name (str)
    178   \         SGData           Space group details as a :ref:`space group (SGData) object <SGData_table>`
    179                              as defined in :func:`GSASIIspc.SpcGroup`.
    180   \         Pawley neg wt    Restraint value for negative Pawley intensities
    181                              (float)
    182   \         Flip             dict of Charge flip controls
     173  \         Color            Colors for atoms (list of (r,b,g) triplets)
     174  \         Compare          dict of polygon comparison parameters
    183175  \         Data plot type   data plot type ('Mustrain', 'Size' or
    184176                             'Preferred orientation') for powder data (str)
    185   \         Mass             Mass of unit cell contents in g/mol
    186   \         POhkl            March-Dollase preferred orientation direction
    187   \         Z                dict of atomic numbers for each atom type
    188   \         vdWRadii         dict of van der Waals radii for each atom type
    189   \         Color            Colors for atoms (list of (r,b,g) triplets)
    190   \         AtomTypes        List of atom types
    191   \         AtomMass         List of masses for atoms
    192   \         doPawley         Flag for Pawley intensity extraction (bool)
    193   \         NoAtoms          Number of atoms per unit cell of each type (dict)
    194   \         Pawley dmin      maximum Q (as d-space) to use for Pawley
    195                              extraction (float)
    196   \         BondRadii        Default radius for each atom used to compute
    197                              interatomic distances (list of floats)
    198   \         AngleRadii       Default radius for each atom used to compute
    199                              interatomic angles (list of floats)
    200177  \         DisAglCtls       Dict with distance/angle search controls,
    201178                             which has keys 'Name', 'AtomTypes',
     
    205182                             a multiplier for bond and angle search range
    206183                             [typically (0.85,0.85)].
     184  \         F000X            x-ray F(000) intensity (float)
     185  \         F000N            neutron F(000) intensity (float)
     186  \         Flip             dict of Charge flip controls
     187  \         HydIds           dict geometrically generated hydrogen atoms
     188  \         Isotope          dict of isotopes for each atom type
     189  \         Isotopes         dict of scattering lengths for each isotope
     190                             combination for each element in phase
     191  \         MCSA controls    Monte Carlo-Simulated Annealing controls (dict)
     192  \         Map              dict of map parameters
     193  \         Mass             Mass of unit cell contents in g/mol
     194  \         Modulated        bool True if phase modulated
     195  \         Mydir            directory of current .gpx file (str)
     196  \         Name             phase name (str)
     197  \         Type             'nuclear' or 'macromolecular' for now (str)
     198  \         NoAtoms          Number of atoms per unit cell of each type (dict)
     199  \         POhkl            March-Dollase preferred orientation direction
     200  \         Pawley dmin      maximum Q (as d-space) to use for Pawley
     201                             extraction (float)
     202  \         Pawley dmax      minimum Q (as d-space) to use for Pawley
     203                             extraction (float)
     204  \         Pawley neg wt    Restraint value for negative Pawley intensities
     205                             (float)
     206  \         SGData           Space group details as a :ref:`space group (SGData) object <SGData_table>`
     207                             as defined in :func:`GSASIIspc.SpcGroup`.
     208  \         SH Texture       dict of spherical harmonic preferred orientation
     209                             parameters
     210  \         Super            int dimension of super group (0,1 only)
     211  \         Type             str phase type (e.g. 'nuclear')
     212  \         Z                dict of atomic numbers for each atom type
     213  \         doDysnomia       bool flag for max ent map modification via Dysnomia
     214  \         doPawley         bool Flag for Pawley intensity extraction
     215  \         vdWRadii         dict of van der Waals radii for each atom type
    207216ranId           \            unique random number Id for phase (int)
    208217pId             \            Phase Id number for current project (int).
     
    213222                             (list of lists)
    214223Drawing         \            Display parameters (dict)
    215 \           ballScale        Size of spheres in ball-and-stick display (float)
    216 \           bondList         dict with bonds
    217 \           contourLevel     map contour level in e/A^3 (float)
    218 \           showABC          Flag to show view point triplet (bool). True=show.
    219 \           viewDir          cartesian viewing direction (np.array with three
    220                              elements)
     224\           Atoms            A list of lists with an entry for each atom
     225                             that is plotted.
     226\           Plane            list Controls for contour density plane display
     227\           Quaternion       Viewing quaternion (4 element np.array)
    221228\           Zclip            clipping distance in A (float)
     229\           Zstep            Step to de/increase Z-clip (float)
     230\           atomPtrs         positions of x, type, site sym, ADP flag in Draw Atoms (list)
    222231\           backColor        background for plot as and R,G,B triplet
    223232                             (default = [0, 0, 0], black).
    224233                             (list with three atoms)
     234\           ballScale        Size of spheres in ball-and-stick display (float)
     235\           bondList         dict with bonds
     236\           bondRadius       Size of binds in A (float)
     237\           cameraPos        Viewing position in A for plot (float)
     238\           contourLevel     map contour level in e/A^3 (float)
     239\           contourMax       float map contour maximum
     240\           depthFog         True if use depthFog on plot - set currently as False (bool)
     241\           ellipseProb      Probability limit for display of thermal
     242                             ellipsoids in % (float).
     243\           magMult          float multiplier for magnetic moment arrows
     244\           mapSize          float x & y dimensions of contourmap (fixed internally)
     245\           modelView        4,4 array from openGL drawing transofmation matrix
     246\           oldxy            previous view point (list with two floats)
     247\           radiusFactor     Distance ratio for searching for bonds. ? Bonds
     248                             are located that are within r(Ra+Rb) and (Ra+Rb)/r
     249                             where Ra and Rb are the atomic radii.
    225250\           selectedAtoms    List of selected atoms (list of int values)
     251\           showABC          Flag to show view point triplet (bool). True=show.
     252\           showHydrogen     Flag to control plotting of H atoms.
    226253\           showRigidBodies  Flag to highlight rigid body placement
     254\           showSlice        flag to show contour map
    227255\           sizeH            Size ratio for H atoms (float)
    228 \           bondRadius       Size of binds in A (float)
    229 \           atomPtrs         positions of x, type, site sym, ADP flag in Draw Atoms (list)
     256\           unitCellBox      Flag to control display of the unit cell.
     257\           vdwScale         Multiplier of van der Waals radius for
     258                             display of vdW spheres.
     259\           viewDir          cartesian viewing direction (np.array with three
     260                             elements)
    230261\           viewPoint        list of lists. First item in list is [x,y,z]
    231262                             in fractional coordinates for the center of
    232263                             the plot. Second item list of previous & current
    233264                             atom number viewed (may be [0,0])
    234 \           showHydrogen     Flag to control plotting of H atoms.
    235 \           unitCellBox      Flag to control display of the unit cell.
    236 \           ellipseProb      Probability limit for display of thermal
    237                              ellipsoids in % (float).
    238 \           vdwScale         Multiplier of van der Waals radius for
    239                              display of vdW spheres.
    240 \           Atoms            A list of lists with an entry for each atom
    241                              that is plotted.
    242 \           Zstep            Step to de/increase Z-clip (float)
    243 \           Quaternion       Viewing quaternion (4 element np.array)
    244 \           radiusFactor     Distance ratio for searching for bonds. ? Bonds
    245                              are located that are within r(Ra+Rb) and (Ra+Rb)/r
    246                              where Ra and Rb are the atomic radii.
    247 \           oldxy            previous view point (list with two floats)
    248 \           cameraPos        Viewing position in A for plot (float)
    249 \           depthFog         True if use depthFog on plot - set currently as False (bool)
    250265RBModels        \            Rigid body assignments (note Rigid body definitions
    251266                             are stored in their own main top-level tree entry.)
     267RMC             \            dict RMCProfile & rmcfull controls
    252268Pawley ref      \            Pawley reflections
    253269Histograms      \            A dict of dicts. The key for the outer dict is
     
    268284\           Mustrain         List of microstrain parameters, in order:
    269285
    270                                0. Type, one of u'generalized', u'isotropic',
    271                                   u'uniaxial'
     286                               0. Type, one of  u'isotropic', u'uniaxial',
     287                                  u'generalized'
    272288                               1. Isotropic/uniaxial parameters - list of 3 floats
    273289                               2. Refinement flags - list of 3 bools
     
    291307\           Scale            Phase fraction, list of [float, bool].
    292308\           Show             bool
     309\           Size             List of crystallite size parameters, in order:
     310   
     311                               0. Type, one of  u'isotropic', u'uniaxial',
     312                                  u'ellipsoidal'
     313                               1. Isotropic/uniaxial parameters - list of 3 floats
     314                               2. Refinement flags - list of 3 bools
     315                               3. Size axis - list of 3 ints, [h, k, l]
     316                               4. Ellipsoidal size parameters - list of 6
     317                                  floats
     318                               5. Ellipsoidal refinement flags - list of bools,
     319                                  corresponding to the parameters of (4)
    293320\           Use              bool
    294321\           newLeBail        Whether to perform a new LeBail extraction
     
    356383Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
    357384and the information is placed in a SGdata object
    358 which is a dict with these keys:
     385which is a dict with these keys. Magnetic ones are marked "mag"
    359386
    360387.. tabularcolumns:: |l|p{4.5in}|
     
    363390  key         explanation
    364391==========  ====================================================
    365 SpGrp       space group symbol (str)
    366 Laue        one of the following 14 Laue classes:
    367             -1, 2/m, mmm, 4/m, 4/mmm, 3R,
    368             3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
     392BNSlattsym  mag - BNS magnetic space group symbol and centering vector
     393GenFlg      mag - list of symmetry generators indices
     394GenSym      mag - list of names for each generator
     395MagMom      mag - list of "time reversals" for each magnetic operator
     396MagPtGp     mag  Magnetic point group symbol
     397MagSpGrp    mag - Magnetic space group symbol
     398OprNames    mag - names for each space group operation
     399SGCen       Symmetry cell centering vectors. A (n,3) np.array
     400            of centers. Will always have at least one row:
     401            ``np.array([[0, 0, 0]])``
     402SGFixed     bool only True if phase mported from a magnetic cif file
     403            then the space group can not be changed by the user because
     404            operator set from cif may be nonstandard
     405SGGen       list of generators
     406SGGray      True if space group is a gray group (incommensurate magnetic structures)
    369407SGInv       True if centrosymmetric, False if not (bool)
    370408SGLatt      Lattice centering type. Will be one of
    371409            P, A, B, C, I, F, R (str)
    372 SGUniq      unique axis if monoclinic. Will be
    373             a, b, or c for monoclinic space groups.
    374             Will be blank for non-monoclinic. (str)
    375 SGCen       Symmetry cell centering vectors. A (n,3) np.array
    376             of centers. Will always have at least one row:
    377             ``np.array([[0, 0, 0]])``
     410SGLaue        one of the following 14 Laue classes:
     411            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
     412            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
    378413SGOps       symmetry operations as a list of form
    379414            ``[[M1,T1], [M2,T2],...]``
     
    384419            are transformed using
    385420            :math:`X^\prime = M_n*X+T_n`
     421SGPolax     Axes for space group polarity. Will be one of
     422            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
     423            'xyz'. In the case where axes are arbitrary
     424            '111' is used (P 1, and ?).
     425SGPtGrp     Point group f the space group
     426SGUniq      unique axis if monoclinic. Will be
     427            a, b, or c for monoclinic space groups.
     428            Will be blank for non-monoclinic. (str)
     429SGSpin      mag - list of spin flip operatiors (+1 or -1) for the space group operations
    386430SGSys       symmetry unit cell: type one of
    387431            'triclinic', 'monoclinic', 'orthorhombic',
    388432            'tetragonal', 'rhombohedral', 'trigonal',
    389433            'hexagonal', 'cubic' (str)
    390 SGPolax     Axes for space group polarity. Will be one of
    391             '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
    392             'xyz'. In the case where axes are arbitrary
    393             '111' is used (P 1, and ?).
     434SSGK1       list of superspace multipliers
     435SpGrp       space group symbol (str)
     436SpnFlp      mag - list of magnetic spin flips for every magnetic space group operator
     437           
    394438==========  ====================================================
    395439
     
    430474are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
    431475which define locations in the atom record, as shown below. Items shown are
    432 always present; additional ones for macromolecular phases are marked 'mm'
     476always present; additional ones for macromolecular phases are marked 'mm',
     477and those for magnetic structures are marked 'mg'
    433478
    434479.. tabularcolumns:: |l|p{4.5in}|
     
    442487ct-1              atom label (str)
    443488ct                atom type (str)
    444 ct+1              refinement flags; combination of 'F', 'X', 'U' (str)
     489ct+1              refinement flags; combination of 'F', 'X', 'U', 'M' (str)
    445490cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
    446491cx+3              site occupancy (float)
     492cx+4,5,6          mg - atom magnetic moment along a,b,c in Bohr magnetons
    447493cs                site symmetry (str)
    448494cs+1              site multiplicity (int)
     
    468514are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
    469515which define locations in the atom record, as shown below. Items shown are
    470 always present; additional ones for macromolecular phases are marked 'mm'
     516always present; additional ones for macromolecular phases are marked 'mm',
     517and those for magnetic structures are marked 'mg'
    471518
    472519.. tabularcolumns:: |l|p{4.5in}|
     
    481528ct                atom type (str)
    482529cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
     530cx+3,4,5          mg - atom magnetic moment along a,b,c in Bohr magnetons
    483531cs-1              Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
    484532cs                atom drawing style; e.g. 'balls & sticks' (str)
     
    528576                                          the :ref:`Powder Reflections <PowderRefl_table>`
    529577                                          description.
    530 Instrument Parameters         \           A list containing two dicts where the possible
    531                                           keys in each dict are listed below. The value
    532                                           for each item is a list containing three values:
    533                                           the initial value, the current value and a
    534                                           refinement flag which can have a value of
     578Instrument Parameters (CW)    \           A list containing two dicts for constant wavelength
     579                                          data where the possible keys in each dict are listed
     580                                          below. The value for each item is a list containing
     581                                          three values: the initial value, the current value
     582                                          and a refinement flag which can have a value of
    535583                                          True, False or 0 where 0 indicates a value that
    536584                                          cannot be refined. The first and second
    537585                                          values are floats unless otherwise noted.
    538586                                          Items in the first dict are noted as [1]
     587\                         Type            Histogram type (str) [1]:
     588                                           * 'PXC' for constant wavelength x-ray
     589                                           * 'PNC' for constant wavelength neutron
     590\                         Bank            Data set number in a multidata file (usually 1)
    539591\                         Lam             Specifies a wavelength in Angstroms [1]
    540592\                         Lam1            Specifies the primary wavelength in
     
    545597                                          source is used [1]
    546598                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]
    547 \                         Type            Histogram type (str) [1]:
    548                                            * 'PXC' for constant wavelength x-ray
    549                                            * 'PNC' for constant wavelength neutron
    550                                            * 'PNT' for time of flight neutron
    551599\                         Zero            Two-theta zero correction in *degrees* [1]
    552600\                         Azimuth         Azimuthal setting angle for data recorded
     
    556604                                          FWHM goes as
    557605                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
    558 \                         X, Y            Cauchy (Lorentzian) instrumental broadening
     606\                         X, Y, Z         Cauchy (Lorentzian) instrumental broadening
    559607                                          coefficients [1]
    560608\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
    561609                                          peak broadening ratio. Note that this is the
    562                                           average between S/L and H/L where S is
     610                                          sum of S/L and H/L where S is
    563611                                          sample height, H is the slit height and
    564612                                          L is the goniometer diameter. [1]
    565613\                         Polariz.        Polarization coefficient. [1]
     614Instrument Parameters (TOF)   \           A list containing two dicts for neutron time-of-flight
     615                                          (TOF) data where the possible keys in each dict are listed
     616                                          below. The value for each item is a list containing
     617                                          three values: the initial value, the current value
     618                                          and a refinement flag which can have a value of
     619                                          True, False or 0 where 0 indicates a value that
     620                                          cannot be refined. The first and second
     621                                          values are floats unless otherwise noted.
     622                                          Items in the first dict are noted as [1]
     623\                         Type            Histogram type (str) [1]:
     624                                           * 'PNT' for time of flight neutron
     625\                         Bank            Data set number in a multidata file
     626\                         2-theta         Nominal scattering angle for the detector
     627\                         fltPath         Total flight path source-sample-detector
     628\                         Azimuth         Azimuth angle for detector righ hand rotation
     629                                          from horizontal away from source
     630\                         difC,difA,difB  Diffractometer constants for conversion of d-spacing to TOF
     631                                          in microseconds
     632\                         Zero            Zero point offset (microseconds)
     633\                         alpha           Exponential rise profile coefficients
     634\                         beta-0          Exponential decay profile coefficients
     635                          beta-1
     636                          beta-q
     637\                         sig-0           Gaussian profile coefficients
     638                          sig-1
     639                          sig-2
     640                          sig-q   
     641\                         X,Y,Z           Lorentzian profile coefficients 
    566642wtFactor                      \           A weighting factor to increase or decrease
    567643                                          the leverage of data in the histogram (float).
     
    652728 11          intensity correction for reflection, this times
    653729             :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
    654  12          Prfo
    655  13          Trans
    656  14          Ext
     730 12          Preferred orientation correction
     731 13          Transmission (absorption correction)
     732 14          Extinction correction
    657733==========  ====================================================
    658734
     
    852928\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
    853929                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
     930\                           SpotMask            dict: 'esdMul'(int) number of standard deviations above mean ring intensity to mask
     931                                                'spotMask' (bool array) the spot mask for every pixel in image         
    854932
    855933Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
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