Changeset 4809 for trunk/GSASIIobj.py


Ignore:
Timestamp:
Feb 10, 2021 3:49:46 PM (10 months ago)
Author:
toby
Message:

display more Residue rigid body info; better docs

File:
1 edited

Legend:

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Added
Removed
  • trunk/GSASIIobj.py

    r4680 r4809  
    454454
    455455
     456Phase Information
     457--------------------
     458
     459.. index::
     460   single: Phase information record description
     461
     462Phase information is placed in one of the following keys:
     463
     464.. tabularcolumns:: |l|p{4.5in}|
     465
     466==========  ==============================================================
     467  key         explanation
     468==========  ==============================================================
     469General       Overall information about a phase
     470Histograms    Information about each histogram linked to the
     471              current phase as well as parameters that
     472              are defined for each histogram and phase
     473              (such as sample peak widths and preferred
     474              orientation parameters.
     475Atoms         Contains a list of atoms, as described in the
     476              :ref:`Atom Records <Atoms_table>` description.
     477Drawing       Parameters that determine how the phase is
     478              displayed, including a list of atoms to be
     479              included, as described in the
     480              :ref:`Drawing Atom Records <Drawing_atoms_table>`
     481              description
     482MCSA          Monte-Carlo simulated annealing parameters
     483pId           The index of each phase in the project, numbered
     484              starting at 0
     485ranId         An int value with a unique value for each phase
     486RBModels      A list of dicts with parameters for each
     487              rigid body inserted into the current phase,
     488              as defined in the
     489              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
     490              Note that the rigid bodies are defined as
     491              :ref:`Rigid Body Objects <RBData_table>`
     492RMC           PDF modeling parameters
     493Pawley ref    Pawley refinement parameters
     494
     495==========  ==============================================================
     496
    456497.. _Atoms_table:
    457498
     
    460501   single: Data object descriptions; Atoms record
    461502
     503--------------------
    462504Atom Records
    463 ------------
     505--------------------
    464506
    465507If ``phasedict`` points to the phase information in the data tree, then
     
    500542   single: Data object descriptions; Drawing atoms record
    501543
     544----------------------------
    502545Drawing Atom Records
    503 --------------------
     546----------------------------
    504547
    505548If ``phasedict`` points to the phase information in the data tree, then
     
    531574cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
    532575ci                  (int) unique atom identifier; matches source atom Id in Atom Records
     576==============   ===================================================================================
     577
     578.. _Rigid_Body_Insertions:
     579
     580----------------------------
     581Rigid Body Insertions
     582----------------------------
     583
     584If ``phasedict`` points to the phase information in the data tree, then
     585rigid body information is contained in list(s) in
     586``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
     587for each rigid body inserted into the current phase.
     588
     589.. tabularcolumns:: |l|p{4.5in}|
     590
     591==============   ===================================================================================
     592key              explanation
     593==============   ===================================================================================
     594fixOrig           Should the origin be fixed (when editing, not the refinement flag)
     595Ids               Ids for assignment of atoms in the rigid body
     596numChain          Chain number for macromolecular fits
     597Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
     598OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
     599Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
     600RBId              References the unique ID of a rigid body in the
     601                  :ref:`Rigid Body Objects <RBData_table>`
     602RBname            The name for the rigid body (str)
     603ThermalMotion     The thermal motion description for the rigid body, which includes a choice for
     604                  the model and can include TLS parameters or an overall Uiso value.
     605Torsions          Defines the torsion angle and refinement flag for each torsion defined in
     606                  the :ref:`Rigid Body Object <RBData_table>`
    533607==============   ===================================================================================
    534608
     
    17131787            lbl = ShortPhaseNames.get(l[0],'phase?')
    17141788            if 'RB' in l[2]:    #rigid body parm
    1715                 s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
     1789                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
    17161790            else: #modulation parm
    17171791                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
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