Changeset 2212

Timestamp:

Apr 14, 2016 3:44:39 PM (8 years ago)

Author:

vondreele

Message:

Implement 'abc*' as one of the 'Common' cell transformations.
Transformations now transforms atom positions & Uijs
Fix problem in ImageGUI where load controls didn't update the image plot correctly.

Location:

trunk

Files:

• GSASIIgrid.py (modified) (6 diffs)
• GSASIIimgGUI.py (modified) (4 diffs)
• GSASIIlattice.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (5 diffs)

trunk/GSASIIgrid.py

@@ -342 +342 @@
         self.Trans = np.eye(3)
         self.Vec = np.zeros(3)
-        self.SpGrp = phase['General']['SGData']['SpGrp']
+        self.oldSpGrp = phase['General']['SGData']['SpGrp']
+        self.oldSGdata = phase['General']['SGData']
+        self.newSpGrp = self.Phase['General']['SGData']['SpGrp']
         self.oldCell = phase['General']['Cell'][1:8]
-        self.newCell = copy.copy(self.oldCell)
+        self.newCell = self.Phase['General']['Cell'][1:8]
         self.Common = 'abc'
         self.Draw()
@@ -365 +367 @@
             Obj = event.GetEventObject()
             self.Common = Obj.GetValue()
-            self.Trans = commonTrans[self.Common]
+            if '*' in self.Common:
+                A,B = G2lat.cell2AB(self.oldCell[:6])
+                self.newCell[2:5] = [A[2,2],90.,90.]
+                a,b = G2lat.cell2AB(self.newCell[:6])
+                self.Trans = np.inner(a.T,B)    #correct!
+                self.newSpGrp = 'P 1'
+                SGErr,SGData = G2spc.SpcGroup(self.newSpGrp)
+                self.Phase['General']['SGData'] = SGData
+            else:
+                self.Trans = commonTrans[self.Common]
             OnTest(event)
        
@@ -373 +384 @@
             for fld in Flds: fld = fld.strip()
             SpcGp = ' '.join(Flds)
-            if SpcGp == self.SpGrp: #didn't change it!
+            if SpcGp == self.newSpGrp: #didn't change it!
                 return
             # try a lookup on the user-supplied name
@@ -383 +394 @@
             if SGErr:
                 text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
-                SGTxt.SetValue(self.SpGrp)
+                SGTxt.SetValue(self.newSpGrp)
                 msg = 'Space Group Error'
                 Style = wx.ICON_EXCLAMATION
@@ -391 +402 @@
                 text,table = G2spc.SGPrint(SGData)
                 self.Phase['General']['SGData'] = SGData
-                self.SpGrp = SpcGp
+                self.newSpGrp = SpcGp
                 SGTxt.SetValue(self.Phase['General']['SGData']['SpGrp'])
                 msg = 'Space Group Information'
@@ -454 +465 @@
         sgSizer = wx.BoxSizer(wx.HORIZONTAL)
         sgSizer.Add(wx.StaticText(self.panel,label='  Space group: '),0,WACV)
-        SGTxt = wx.TextCtrl(self.panel,value=self.SpGrp,style=wx.TE_PROCESS_ENTER)
+        SGTxt = wx.TextCtrl(self.panel,value=self.newSpGrp,style=wx.TE_PROCESS_ENTER)
         SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
         SGTxt.Bind(wx.EVT_KILL_FOCUS,OnSpaceGroup)

trunk/GSASIIimgGUI.py

@@ -22 +22 @@
 import math
 import time
-import copy
 import sys
 import wx
@@ -173 +172 @@
         G2plt.PlotExposedImage(G2frame,event=event)
             
+    def ResetThresholds():
+        Imin = max(0.,np.min(G2frame.ImageZ))
+        Imax = np.max(G2frame.ImageZ)
+        data['range'] = [(Imin,Imax),[Imin,Imax]]
+        masks['Thresholds'] = [(Imin,Imax),[Imin,Imax]]
+        MaxSizer.GetChildren()[2].Window.SetValue(str(int(Imax)))   #tricky 
+        MaxSizer.GetChildren()[5].Window.SetValue(str(int(Imin)))   #tricky
+         
     def OnIntegrate(event):
         '''Integrate image in response to a menu event or from the AutoIntegrate
@@ -358 +365 @@
         finally:
             dlg.Destroy()
+        G2frame.ImageZ = GetImageZ(G2frame,data)
+        ResetThresholds()
         G2plt.PlotExposedImage(G2frame,event=event)
         wx.CallLater(100,UpdateImageControls,G2frame,data,masks)
@@ -814 +823 @@
     def BackSizer():
         
-        def ResetThresholds():
-            Imin = max(0.,np.min(G2frame.ImageZ))
-            Imax = np.max(G2frame.ImageZ)
-            data['range'] = [(Imin,Imax),[Imin,Imax]]
-            masks['Thresholds'] = [(Imin,Imax),[Imin,Imax]]
-            MaxSizer.GetChildren()[2].Window.SetValue(str(int(Imax)))   #tricky 
-            MaxSizer.GetChildren()[5].Window.SetValue(str(int(Imin)))   #tricky 
-        
         def OnBackImage(event):
             data['background image'][0] = backImage.GetValue()

trunk/GSASIIlattice.py

@@ -31 +31 @@
 ########### SVN repository information ###################
 import math
+import copy
+import sys
+import random as ran
 import numpy as np
 import numpy.linalg as nl
@@ -225 +228 @@
     Uij = np.inner(Trans,np.inner(U6toUij(U6),Trans))
     return UijtoU6(Uij)
-           
+    
+def TransformPhase(oldPhase,newPhase,Trans,Vec):
+    '''Transform atoms from oldPhase to newPhase by Trans & Vec
+    
+    :param oldPhase: dict G2 phase info for old phase
+    :param newPhase: dict G2 phase info for new phase; with new cell & space group
+            atoms are from oldPhase & will be transformed
+    :param Trans: array transformation matrix
+    :param Vec: array transformation vector
+    '''
+    
+    cx,ct,cs,cia = oldPhase['General']['AtomPtrs']
+    SGData = newPhase['General']['SGData']
+    invTrans = nl.inv(Trans)
+    newAtoms = FillUnitCell(oldPhase)
+    for atom in newAtoms:
+        atom[cx:cx+3] = TransformXYZ(atom[cx:cx+3],invTrans.T,Vec)
+        if atom[cia] == 'A':
+            atom[cia+2:cia+8] = TransformU6(atom[cia+2:cia+8],invTrans)
+        atom[cs:cs+2] = G2spc.SytSym(atom[cx:cx+3],SGData)
+        atom[cia+8] = ran.randint(0,sys.maxint)
+    newPhase['Atoms'] = newAtoms
+#   GetUnique(newPhase)
+    return newPhase
+    
+    
+def FillUnitCell(Phase):
+    atomData = copy.deepcopy(Phase['Atoms'])
+    nAtoms = len(atomData)
+    SGData = Phase['General']['SGData']
+    cx,ct,cs,cia = Phase['General']['AtomPtrs']
+    for atom in atomData[:nAtoms]:
+        XYZ = np.array(atom[cx:cx+3])
+        if atom[cia] == 'A':
+            Uij = atom[cia+2:cia+8]
+            result = G2spc.GenAtom(XYZ,SGData,False,Uij,True)
+            for item in result:
+                atom[cx:cx+3] = item[0]
+                atom[cia+2:cia+8] = item[1]
+                atomData.append(atom[:cia+9])  #not SS stuff
+        else:
+            result = G2spc.GenAtom(XYZ,SGData,False,Move=True)
+            for item in result:
+                atom[cx:cx+3] = item[0]
+                atomData.append(atom[:cia+9])  #not SS stuff
+    return atomData
+       
+def GetUnique(Phase):
+    pass
+#    def noDuplicate(xyz,peaks,Amat):
+#        if True in [np.allclose(np.inner(Amat,xyz),np.inner(Amat,peak),atol=0.5) for peak in peaks]:
+#            return False
+#        return True
+#                            
+#    generalData = data['General']
+#    cell = generalData['Cell'][1:7]
+#    Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
+#    A = G2lat.cell2A(cell)
+#    SGData = generalData['SGData']
+#    mapPeaks = data['Map Peaks']
+#    Indx = {}
+#    XYZ = {}
+#    for ind in Ind:
+#        XYZ[ind] = np.array(mapPeaks[ind][1:4])
+#        Indx[ind] = True
+#    for ind in Ind:
+#        if Indx[ind]:
+#            xyz = XYZ[ind]
+#            for jnd in Ind:
+#                if ind != jnd and Indx[jnd]:                        
+#                    Equiv = G2spc.GenAtom(XYZ[jnd],SGData,Move=True)
+#                    xyzs = np.array([equiv[0] for equiv in Equiv])
+#                    Indx[jnd] = noDuplicate(xyz,xyzs,Amat)
+#    Ind = []
+#    for ind in Indx:
+#        if Indx[ind]:
+#            Ind.append(ind)
+#    return Ind
+
+
+            
 def calc_rVsq(A):
     """Compute the square of the reciprocal lattice volume (1/V**2) from A'

trunk/GSASIIphsGUI.py

@@ -1227 +1227 @@
             dlg.Destroy()
         phaseName = newPhase['General']['Name']
-        print phaseName
+        newPhase = G2lat.TransformPhase(data,newPhase,Trans,Vec)
         sub = G2frame.PatternTree.AppendItem(parent=
             G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Phases'),text=phaseName)

trunk/GSASIIplot.py

@@ -126 +126 @@
             attribs = (wx.glcanvas.WX_GL_DOUBLEBUFFER,)
             self.canvas = wx.glcanvas.GLCanvas(self,-1,attribList=attribs,**kwargs)
-        # create GL context for wx > 2.8
+        # create GL context
         i,j= wx.__version__.split('.')[0:2]
         if int(i)+int(j)/10. > 2.8:
@@ -1113 +1113 @@
         RenderDots(HKL,RC)
         time0 = time.time()
-        if Page.context: Page.canvas.SetCurrent(Page.context)    # wx 2.9 fix
+        if Page.context: Page.canvas.SetCurrent(Page.context)
         Page.canvas.SwapBuffers()
 
@@ -5656 +5656 @@
                 RenderBackbone(Backbone,BackboneColor,bondR)
 #        print time.time()-time0
-        if Page.context: Page.canvas.SetCurrent(Page.context)    # wx 2.9 fix
+        if Page.context: Page.canvas.SetCurrent(Page.context)
         Page.canvas.SwapBuffers()
         
@@ -5963 +5963 @@
             RenderBonds(x,y,z,Bonds[iat],0.05,color)
             RenderLabel(x,y,z,'  '+atNames[iat],matRot)
-        if Page.context: Page.canvas.SetCurrent(Page.context)    # wx 2.9 fix
+        if Page.context: Page.canvas.SetCurrent(Page.context)
         Page.canvas.SwapBuffers()
 
@@ -6349 +6349 @@
             if Page.labels:
                 RenderLabel(x,y,z,'  '+AtNames[iat],matRot)
-        if Page.context: Page.canvas.SetCurrent(Page.context)    # wx 2.9 fix
+        if Page.context: Page.canvas.SetCurrent(Page.context)
         Page.canvas.SwapBuffers()