Changeset 4809

Timestamp:

Feb 10, 2021 3:49:46 PM (2 years ago)

Author:

toby

Message:

display more Residue rigid body info; better docs

Location:

trunk

Files:

• GSASIIconstrGUI.py (modified) (1 diff)
• GSASIIdataGUI.py (modified) (2 diffs)
• GSASIIobj.py (modified) (5 diffs)
• GSASIIphsGUI.py (modified) (9 diffs)

trunk/GSASIIconstrGUI.py

@@ -3292 +3292 @@
                     Indx[stripH.GetId()] = rbid
                     nameSizer.Add(stripH,0,WACV)
+            nameSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'  body type #'+
+                                        str(data['RBIds']['Residue'].index(rbid))),0,WACV)
             return nameSizer
             

trunk/GSASIIdataGUI.py

@@ -8528 +8528 @@
     mainSizer.Add((5,5),)
     wtSizer = wx.BoxSizer(wx.HORIZONTAL)
-    wtSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
     wtSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Weight factor: '),0,WACV)
     wtSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[0],'wtFactor',nDig=(10,3),xmin=1.e-9),0,WACV)
@@ -8539 +8538 @@
 #        comp.Bind(wx.EVT_COMBOBOX, OnCompression)
 #        wtSizer.Add(comp,0,WACV)
-
-    mainSizer.Add(wtSizer)
+    wtSizer.Add((-1,-1),1,wx.EXPAND)
+    wtSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
+    mainSizer.Add(wtSizer,0,wx.EXPAND)
     wtSizer = wx.BoxSizer(wx.HORIZONTAL)
     wtSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Histogram label: '),0,WACV)

trunk/GSASIIobj.py

@@ -454 +454 @@
 
 
+Phase Information
+--------------------
+
+.. index::
+   single: Phase information record description
+
+Phase information is placed in one of the following keys:
+
+.. tabularcolumns:: |l|p{4.5in}|
+
+==========  ==============================================================
+  key         explanation
+==========  ==============================================================
+General       Overall information about a phase
+Histograms    Information about each histogram linked to the 
+              current phase as well as parameters that 
+              are defined for each histogram and phase
+              (such as sample peak widths and preferred 
+              orientation parameters. 
+Atoms         Contains a list of atoms, as described in the 
+              :ref:`Atom Records <Atoms_table>` description.
+Drawing       Parameters that determine how the phase is 
+              displayed, including a list of atoms to be 
+              included, as described in the 
+              :ref:`Drawing Atom Records <Drawing_atoms_table>`
+              description
+MCSA          Monte-Carlo simulated annealing parameters
+pId           The index of each phase in the project, numbered
+              starting at 0
+ranId         An int value with a unique value for each phase 
+RBModels      A list of dicts with parameters for each 
+              rigid body inserted into the current phase, 
+              as defined in the 
+              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
+              Note that the rigid bodies are defined as 
+              :ref:`Rigid Body Objects <RBData_table>` 
+RMC           PDF modeling parameters
+Pawley ref    Pawley refinement parameters 
+
+==========  ==============================================================
+
 .. _Atoms_table:
 
@@ -460 +501 @@
    single: Data object descriptions; Atoms record
 
+--------------------
 Atom Records
-------------
+--------------------
 
 If ``phasedict`` points to the phase information in the data tree, then
@@ -500 +542 @@
    single: Data object descriptions; Drawing atoms record
 
+----------------------------
 Drawing Atom Records
---------------------
+----------------------------
 
 If ``phasedict`` points to the phase information in the data tree, then
@@ -531 +574 @@
 cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23 
 ci                  (int) unique atom identifier; matches source atom Id in Atom Records 
+==============   ===================================================================================
+
+.. _Rigid_Body_Insertions:
+
+----------------------------
+Rigid Body Insertions
+----------------------------
+
+If ``phasedict`` points to the phase information in the data tree, then
+rigid body information is contained in list(s) in
+``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
+for each rigid body inserted into the current phase. 
+
+.. tabularcolumns:: |l|p{4.5in}|
+
+==============   ===================================================================================
+key              explanation
+==============   ===================================================================================
+fixOrig           Should the origin be fixed (when editing, not the refinement flag)
+Ids               Ids for assignment of atoms in the rigid body
+numChain          Chain number for macromolecular fits 
+Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
+OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
+Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
+RBId              References the unique ID of a rigid body in the 
+                  :ref:`Rigid Body Objects <RBData_table>`
+RBname            The name for the rigid body (str)
+ThermalMotion     The thermal motion description for the rigid body, which includes a choice for 
+                  the model and can include TLS parameters or an overall Uiso value. 
+Torsions          Defines the torsion angle and refinement flag for each torsion defined in 
+                  the :ref:`Rigid Body Object <RBData_table>`
 ==============   ===================================================================================
 
@@ -1713 +1787 @@
             lbl = ShortPhaseNames.get(l[0],'phase?')
             if 'RB' in l[2]:    #rigid body parm
-                s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
+                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
             else: #modulation parm
                 s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)

trunk/GSASIIphsGUI.py

@@ -89 +89 @@
 acosd = lambda x: 180.*np.arccos(x)/np.pi
 atan2d = lambda x,y: 180.*np.arctan2(y,x)/np.pi
+
+# previous rigid body selections
+prevResId = None
+prevVecId = None
 
 if '2' in platform.python_version_tuple()[0]:
@@ -9806 +9810 @@
         Note that the page is a ScrolledWindow, not a Grid
         '''
+        resVarLookup = []
         def OnThermSel(event):       #needs to be seen by VecRbSizer!
             Obj = event.GetEventObject()
@@ -9955 +9960 @@
             return rbSizer
                          
-        def ResrbSizer(RBObj):
-            
+        def ResrbSizer(RBObj,resIndx):
+            '''Displays details for selected rigid body'''
             def OnTorsionRef(event):
                 Obj = event.GetEventObject()
@@ -10005 +10010 @@
                 topLine.Add(wx.StaticText(RigidBodies,-1,
                     '   Rigid body {} axis is aligned along oriention vector'.format(lbl)),0,WACV)
+            varname = str(data['pId'])+'::RBRxxx:'+resVarLookup[resIndx]
+            topLine.Add(wx.StaticText(RigidBodies,-1,
+                    '  (variables '+varname+')'),0,WACV)
             resrbSizer.Add(topLine)
             resrbSizer.Add(LocationSizer(RBObj,'Residue'))
@@ -10073 +10081 @@
         
         def OnVecSelect(event):
-            rbId = select.GetSelection()
-            wx.CallLater(100,RepaintRBInfo,'Vector',rbId)
+            global prevVecId
+            prevVecId = select.GetSelection()
+            wx.CallLater(100,RepaintRBInfo,'Vector',prevVecId)
            
         def OnResSelect(event):
-            rbId = resSelect.GetSelection()
-            wx.CallLater(100,RepaintRBInfo,'Residue',rbId)
+            global prevResId
+            prevResId = resSelect.GetSelection()
+            wx.CallLater(100,RepaintRBInfo,'Residue',prevResId)
            
-        def RepaintRBInfo(rbType,rbId,Scroll=0):
+        def RepaintRBInfo(rbType,rbIndx,Scroll=0):
             oldFocus = wx.Window.FindFocus()
             if 'phoenix' in wx.version():
@@ -10087 +10097 @@
                 G2frame.bottomSizer.DeleteWindows()
             Indx.clear()
-            rbObj = data['RBModels'][rbType][rbId]
+            rbObj = data['RBModels'][rbType][rbIndx]
             data['Drawing']['viewPoint'][0] = rbObj['Orig'][0]
             Quad = rbObj['Orient'][0]
             data['Drawing']['Quaternion'] = G2mth.invQ(Quad)
-            G2frame.bottomSizer =  ResrbSizer(rbObj)
+            G2frame.bottomSizer =  ResrbSizer(rbObj,rbIndx)
             mainSizer.Add(G2frame.bottomSizer)
             mainSizer.Layout()
@@ -10132 +10142 @@
             mainSizer.Add((5,5),0)
             RBnames = []
-            for RBObj in data['RBModels']['Residue']:
-                RBnames.append(RBObj['RBname']+RBObj['numChain'])
-            if resId is None:
+            resVarLookup = []
+            for irb,RBObj in enumerate(data['RBModels']['Residue']):
+                name = RBObj['RBname']+RBObj['numChain']
+                RBnames.append(name)
+                jrb = RBData['RBIds']['Residue'].index(RBObj['RBId'])
+                resVarLookup.append(str(irb)+':'+str(jrb)) # var name suffix following G2strMath.ApplyRBModels()
+            if prevResId is not None:
+                resId = prevResId
+            try:
+                rbName = RBnames[resId]
+            except TypeError:
                 resId = 0
-            rbName = RBnames[resId]
+                rbName = RBnames[resId]
             rbObj = data['RBModels']['Residue'][resId]
             data['Drawing']['viewPoint'][0] = rbObj['Orig'][0]
@@ -10146 +10164 @@
             mainSizer.Add(resSelect,0)
             G2frame.bottomSizer = wx.BoxSizer(wx.VERTICAL)
-            G2frame.bottomSizer.Add(ResrbSizer(rbObj))
+            G2frame.bottomSizer.Add(ResrbSizer(rbObj,resId))
             mainSizer.Add(G2frame.bottomSizer)
             G2plt.PlotStructure(G2frame,data)
@@ -10158 +10176 @@
             for RBObj in data['RBModels']['Vector']:
                 RBnames.append(RBObj['RBname'])
-            if vecId is None:
+            if prevVecId is not None:
+                vecId = prevVecId
+            try:
+                rbName = RBnames[vecId]
+            except TypeError:
                 vecId = 0
-            rbName = RBnames[vecId]
+                rbName = RBnames[vecId]
             rbObj = data['RBModels']['Vector'][vecId]
             data['Drawing']['viewPoint'][0] = rbObj['Orig'][0]