Index: /trunk/GSASIIobj.py
===================================================================
--- /trunk/GSASIIobj.py (revision 4305)
+++ /trunk/GSASIIobj.py (revision 4306)
@@ -158,44 +158,21 @@
========== =============== ====================================================
General \ Overall information for the phase (dict)
- \ AtomPtrs list of four locations to use to pull info
+ \ 3Dproj projections for 3D pole distribution plots
+ \ AngleRadii Default radius for each atom used to compute
+ interatomic angles (list of floats)
+ \ AtomMass List of masses for atoms
+ \ AtomPtrs list of four locations (cx,ct,cs & cu) to use to pull info
from the atom records (list)
- \ F000X x-ray F(000) intensity (float)
- \ F000N neutron F(000) intensity (float)
- \ Mydir directory of current .gpx file (str)
- \ MCSA controls Monte Carlo-Simulated Annealing controls (dict)
+ \ AtomTypes List of atom types
+ \ BondRadii Default radius for each atom used to compute
+ interatomic distances (list of floats)
\ Cell List with 8 items: cell refinement flag (bool)
a, b, c, (Angstrom, float)
alpha, beta & gamma (degrees, float)
volume (A^3, float)
- \ Type 'nuclear' or 'macromolecular' for now (str)
- \ Map dict of map parameters
- \ SH Texture dict of spherical harmonic preferred orientation
- parameters
- \ Isotope dict of isotopes for each atom type
- \ Isotopes dict of scattering lengths for each isotope
- combination for each element in phase
- \ Name phase name (str)
- \ SGData Space group details as a :ref:`space group (SGData) object `
- as defined in :func:`GSASIIspc.SpcGroup`.
- \ Pawley neg wt Restraint value for negative Pawley intensities
- (float)
- \ Flip dict of Charge flip controls
+ \ Color Colors for atoms (list of (r,b,g) triplets)
+ \ Compare dict of polygon comparison parameters
\ Data plot type data plot type ('Mustrain', 'Size' or
'Preferred orientation') for powder data (str)
- \ Mass Mass of unit cell contents in g/mol
- \ POhkl March-Dollase preferred orientation direction
- \ Z dict of atomic numbers for each atom type
- \ vdWRadii dict of van der Waals radii for each atom type
- \ Color Colors for atoms (list of (r,b,g) triplets)
- \ AtomTypes List of atom types
- \ AtomMass List of masses for atoms
- \ doPawley Flag for Pawley intensity extraction (bool)
- \ NoAtoms Number of atoms per unit cell of each type (dict)
- \ Pawley dmin maximum Q (as d-space) to use for Pawley
- extraction (float)
- \ BondRadii Default radius for each atom used to compute
- interatomic distances (list of floats)
- \ AngleRadii Default radius for each atom used to compute
- interatomic angles (list of floats)
\ DisAglCtls Dict with distance/angle search controls,
which has keys 'Name', 'AtomTypes',
@@ -205,4 +182,36 @@
a multiplier for bond and angle search range
[typically (0.85,0.85)].
+ \ F000X x-ray F(000) intensity (float)
+ \ F000N neutron F(000) intensity (float)
+ \ Flip dict of Charge flip controls
+ \ HydIds dict geometrically generated hydrogen atoms
+ \ Isotope dict of isotopes for each atom type
+ \ Isotopes dict of scattering lengths for each isotope
+ combination for each element in phase
+ \ MCSA controls Monte Carlo-Simulated Annealing controls (dict)
+ \ Map dict of map parameters
+ \ Mass Mass of unit cell contents in g/mol
+ \ Modulated bool True if phase modulated
+ \ Mydir directory of current .gpx file (str)
+ \ Name phase name (str)
+ \ Type 'nuclear' or 'macromolecular' for now (str)
+ \ NoAtoms Number of atoms per unit cell of each type (dict)
+ \ POhkl March-Dollase preferred orientation direction
+ \ Pawley dmin maximum Q (as d-space) to use for Pawley
+ extraction (float)
+ \ Pawley dmax minimum Q (as d-space) to use for Pawley
+ extraction (float)
+ \ Pawley neg wt Restraint value for negative Pawley intensities
+ (float)
+ \ SGData Space group details as a :ref:`space group (SGData) object `
+ as defined in :func:`GSASIIspc.SpcGroup`.
+ \ SH Texture dict of spherical harmonic preferred orientation
+ parameters
+ \ Super int dimension of super group (0,1 only)
+ \ Type str phase type (e.g. 'nuclear')
+ \ Z dict of atomic numbers for each atom type
+ \ doDysnomia bool flag for max ent map modification via Dysnomia
+ \ doPawley bool Flag for Pawley intensity extraction
+ \ vdWRadii dict of van der Waals radii for each atom type
ranId \ unique random number Id for phase (int)
pId \ Phase Id number for current project (int).
@@ -213,41 +222,48 @@
(list of lists)
Drawing \ Display parameters (dict)
-\ ballScale Size of spheres in ball-and-stick display (float)
-\ bondList dict with bonds
-\ contourLevel map contour level in e/A^3 (float)
-\ showABC Flag to show view point triplet (bool). True=show.
-\ viewDir cartesian viewing direction (np.array with three
- elements)
+\ Atoms A list of lists with an entry for each atom
+ that is plotted.
+\ Plane list Controls for contour density plane display
+\ Quaternion Viewing quaternion (4 element np.array)
\ Zclip clipping distance in A (float)
+\ Zstep Step to de/increase Z-clip (float)
+\ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list)
\ backColor background for plot as and R,G,B triplet
(default = [0, 0, 0], black).
(list with three atoms)
+\ ballScale Size of spheres in ball-and-stick display (float)
+\ bondList dict with bonds
+\ bondRadius Size of binds in A (float)
+\ cameraPos Viewing position in A for plot (float)
+\ contourLevel map contour level in e/A^3 (float)
+\ contourMax float map contour maximum
+\ depthFog True if use depthFog on plot - set currently as False (bool)
+\ ellipseProb Probability limit for display of thermal
+ ellipsoids in % (float).
+\ magMult float multiplier for magnetic moment arrows
+\ mapSize float x & y dimensions of contourmap (fixed internally)
+\ modelView 4,4 array from openGL drawing transofmation matrix
+\ oldxy previous view point (list with two floats)
+\ radiusFactor Distance ratio for searching for bonds. ? Bonds
+ are located that are within r(Ra+Rb) and (Ra+Rb)/r
+ where Ra and Rb are the atomic radii.
\ selectedAtoms List of selected atoms (list of int values)
+\ showABC Flag to show view point triplet (bool). True=show.
+\ showHydrogen Flag to control plotting of H atoms.
\ showRigidBodies Flag to highlight rigid body placement
+\ showSlice flag to show contour map
\ sizeH Size ratio for H atoms (float)
-\ bondRadius Size of binds in A (float)
-\ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list)
+\ unitCellBox Flag to control display of the unit cell.
+\ vdwScale Multiplier of van der Waals radius for
+ display of vdW spheres.
+\ viewDir cartesian viewing direction (np.array with three
+ elements)
\ viewPoint list of lists. First item in list is [x,y,z]
in fractional coordinates for the center of
the plot. Second item list of previous & current
atom number viewed (may be [0,0])
-\ showHydrogen Flag to control plotting of H atoms.
-\ unitCellBox Flag to control display of the unit cell.
-\ ellipseProb Probability limit for display of thermal
- ellipsoids in % (float).
-\ vdwScale Multiplier of van der Waals radius for
- display of vdW spheres.
-\ Atoms A list of lists with an entry for each atom
- that is plotted.
-\ Zstep Step to de/increase Z-clip (float)
-\ Quaternion Viewing quaternion (4 element np.array)
-\ radiusFactor Distance ratio for searching for bonds. ? Bonds
- are located that are within r(Ra+Rb) and (Ra+Rb)/r
- where Ra and Rb are the atomic radii.
-\ oldxy previous view point (list with two floats)
-\ cameraPos Viewing position in A for plot (float)
-\ depthFog True if use depthFog on plot - set currently as False (bool)
RBModels \ Rigid body assignments (note Rigid body definitions
are stored in their own main top-level tree entry.)
+RMC \ dict RMCProfile & rmcfull controls
Pawley ref \ Pawley reflections
Histograms \ A dict of dicts. The key for the outer dict is
@@ -268,6 +284,6 @@
\ Mustrain List of microstrain parameters, in order:
- 0. Type, one of u'generalized', u'isotropic',
- u'uniaxial'
+ 0. Type, one of u'isotropic', u'uniaxial',
+ u'generalized'
1. Isotropic/uniaxial parameters - list of 3 floats
2. Refinement flags - list of 3 bools
@@ -291,4 +307,15 @@
\ Scale Phase fraction, list of [float, bool].
\ Show bool
+\ Size List of crystallite size parameters, in order:
+
+ 0. Type, one of u'isotropic', u'uniaxial',
+ u'ellipsoidal'
+ 1. Isotropic/uniaxial parameters - list of 3 floats
+ 2. Refinement flags - list of 3 bools
+ 3. Size axis - list of 3 ints, [h, k, l]
+ 4. Ellipsoidal size parameters - list of 6
+ floats
+ 5. Ellipsoidal refinement flags - list of bools,
+ corresponding to the parameters of (4)
\ Use bool
\ newLeBail Whether to perform a new LeBail extraction
@@ -356,5 +383,5 @@
Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
and the information is placed in a SGdata object
-which is a dict with these keys:
+which is a dict with these keys. Magnetic ones are marked "mag"
.. tabularcolumns:: |l|p{4.5in}|
@@ -363,17 +390,25 @@
key explanation
========== ====================================================
-SpGrp space group symbol (str)
-Laue one of the following 14 Laue classes:
- -1, 2/m, mmm, 4/m, 4/mmm, 3R,
- 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
+BNSlattsym mag - BNS magnetic space group symbol and centering vector
+GenFlg mag - list of symmetry generators indices
+GenSym mag - list of names for each generator
+MagMom mag - list of "time reversals" for each magnetic operator
+MagPtGp mag Magnetic point group symbol
+MagSpGrp mag - Magnetic space group symbol
+OprNames mag - names for each space group operation
+SGCen Symmetry cell centering vectors. A (n,3) np.array
+ of centers. Will always have at least one row:
+ ``np.array([[0, 0, 0]])``
+SGFixed bool only True if phase mported from a magnetic cif file
+ then the space group can not be changed by the user because
+ operator set from cif may be nonstandard
+SGGen list of generators
+SGGray True if space group is a gray group (incommensurate magnetic structures)
SGInv True if centrosymmetric, False if not (bool)
SGLatt Lattice centering type. Will be one of
P, A, B, C, I, F, R (str)
-SGUniq unique axis if monoclinic. Will be
- a, b, or c for monoclinic space groups.
- Will be blank for non-monoclinic. (str)
-SGCen Symmetry cell centering vectors. A (n,3) np.array
- of centers. Will always have at least one row:
- ``np.array([[0, 0, 0]])``
+SGLaue one of the following 14 Laue classes:
+ -1, 2/m, mmm, 4/m, 4/mmm, 3R,
+ 3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
SGOps symmetry operations as a list of form
``[[M1,T1], [M2,T2],...]``
@@ -384,12 +419,21 @@
are transformed using
:math:`X^\prime = M_n*X+T_n`
+SGPolax Axes for space group polarity. Will be one of
+ '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
+ 'xyz'. In the case where axes are arbitrary
+ '111' is used (P 1, and ?).
+SGPtGrp Point group f the space group
+SGUniq unique axis if monoclinic. Will be
+ a, b, or c for monoclinic space groups.
+ Will be blank for non-monoclinic. (str)
+SGSpin mag - list of spin flip operatiors (+1 or -1) for the space group operations
SGSys symmetry unit cell: type one of
'triclinic', 'monoclinic', 'orthorhombic',
'tetragonal', 'rhombohedral', 'trigonal',
'hexagonal', 'cubic' (str)
-SGPolax Axes for space group polarity. Will be one of
- '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
- 'xyz'. In the case where axes are arbitrary
- '111' is used (P 1, and ?).
+SSGK1 list of superspace multipliers
+SpGrp space group symbol (str)
+SpnFlp mag - list of magnetic spin flips for every magnetic space group operator
+
========== ====================================================
@@ -430,5 +474,6 @@
are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
which define locations in the atom record, as shown below. Items shown are
-always present; additional ones for macromolecular phases are marked 'mm'
+always present; additional ones for macromolecular phases are marked 'mm',
+and those for magnetic structures are marked 'mg'
.. tabularcolumns:: |l|p{4.5in}|
@@ -442,7 +487,8 @@
ct-1 atom label (str)
ct atom type (str)
-ct+1 refinement flags; combination of 'F', 'X', 'U' (str)
+ct+1 refinement flags; combination of 'F', 'X', 'U', 'M' (str)
cx,cx+1,cx+2 the x,y and z coordinates (3 floats)
cx+3 site occupancy (float)
+cx+4,5,6 mg - atom magnetic moment along a,b,c in Bohr magnetons
cs site symmetry (str)
cs+1 site multiplicity (int)
@@ -468,5 +514,6 @@
are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
which define locations in the atom record, as shown below. Items shown are
-always present; additional ones for macromolecular phases are marked 'mm'
+always present; additional ones for macromolecular phases are marked 'mm',
+and those for magnetic structures are marked 'mg'
.. tabularcolumns:: |l|p{4.5in}|
@@ -481,4 +528,5 @@
ct atom type (str)
cx,cx+1,cx+2 the x,y and z coordinates (3 floats)
+cx+3,4,5 mg - atom magnetic moment along a,b,c in Bohr magnetons
cs-1 Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
cs atom drawing style; e.g. 'balls & sticks' (str)
@@ -528,13 +576,17 @@
the :ref:`Powder Reflections `
description.
-Instrument Parameters \ A list containing two dicts where the possible
- keys in each dict are listed below. The value
- for each item is a list containing three values:
- the initial value, the current value and a
- refinement flag which can have a value of
+Instrument Parameters (CW) \ A list containing two dicts for constant wavelength
+ data where the possible keys in each dict are listed
+ below. The value for each item is a list containing
+ three values: the initial value, the current value
+ and a refinement flag which can have a value of
True, False or 0 where 0 indicates a value that
cannot be refined. The first and second
values are floats unless otherwise noted.
Items in the first dict are noted as [1]
+\ Type Histogram type (str) [1]:
+ * 'PXC' for constant wavelength x-ray
+ * 'PNC' for constant wavelength neutron
+\ Bank Data set number in a multidata file (usually 1)
\ Lam Specifies a wavelength in Angstroms [1]
\ Lam1 Specifies the primary wavelength in
@@ -545,8 +597,4 @@
source is used [1]
I(L2)/I(L1) Ratio of Lam2 to Lam1 [1]
-\ Type Histogram type (str) [1]:
- * 'PXC' for constant wavelength x-ray
- * 'PNC' for constant wavelength neutron
- * 'PNT' for time of flight neutron
\ Zero Two-theta zero correction in *degrees* [1]
\ Azimuth Azimuthal setting angle for data recorded
@@ -556,12 +604,40 @@
FWHM goes as
:math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
-\ X, Y Cauchy (Lorentzian) instrumental broadening
+\ X, Y, Z Cauchy (Lorentzian) instrumental broadening
coefficients [1]
\ SH/L Variant of the Finger-Cox-Jephcoat asymmetric
peak broadening ratio. Note that this is the
- average between S/L and H/L where S is
+ sum of S/L and H/L where S is
sample height, H is the slit height and
L is the goniometer diameter. [1]
\ Polariz. Polarization coefficient. [1]
+Instrument Parameters (TOF) \ A list containing two dicts for neutron time-of-flight
+ (TOF) data where the possible keys in each dict are listed
+ below. The value for each item is a list containing
+ three values: the initial value, the current value
+ and a refinement flag which can have a value of
+ True, False or 0 where 0 indicates a value that
+ cannot be refined. The first and second
+ values are floats unless otherwise noted.
+ Items in the first dict are noted as [1]
+\ Type Histogram type (str) [1]:
+ * 'PNT' for time of flight neutron
+\ Bank Data set number in a multidata file
+\ 2-theta Nominal scattering angle for the detector
+\ fltPath Total flight path source-sample-detector
+\ Azimuth Azimuth angle for detector righ hand rotation
+ from horizontal away from source
+\ difC,difA,difB Diffractometer constants for conversion of d-spacing to TOF
+ in microseconds
+\ Zero Zero point offset (microseconds)
+\ alpha Exponential rise profile coefficients
+\ beta-0 Exponential decay profile coefficients
+ beta-1
+ beta-q
+\ sig-0 Gaussian profile coefficients
+ sig-1
+ sig-2
+ sig-q
+\ X,Y,Z Lorentzian profile coefficients
wtFactor \ A weighting factor to increase or decrease
the leverage of data in the histogram (float).
@@ -652,7 +728,7 @@
11 intensity correction for reflection, this times
:math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
- 12 Prfo
- 13 Trans
- 14 ExtP
+ 12 Preferred orientation correction
+ 13 Transmission (absorption correction)
+ 14 Extinction correction
========== ====================================================
@@ -852,4 +928,6 @@
\ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
in integrsation. The tuple is the image intensity limits and the list are those set by the user.
+\ SpotMask dict: 'esdMul'(int) number of standard deviations above mean ring intensity to mask
+ 'spotMask' (bool array) the spot mask for every pixel in image
Stress/Strain Sample phi (float) Sample rotation about vertical axis.