Changeset 721

Timestamp:

Aug 19, 2012 2:13:13 PM (13 years ago)

Author:

vondreele

Message:

add dist/angle calc for map peaks
unique peaks selects unique set from selected map PeaksUnique?
peaks falling near special positions are corrected to be on special position

Location:

trunk

Files:

• GSASIIgrid.py (modified) (3 diffs)
• GSASIImath.py (modified) (6 diffs)
• GSASIIphsGUI.py (modified) (10 diffs)
• GSASIIplot.py (modified) (4 diffs)

trunk/GSASIIgrid.py ¶

@@ -39 +39 @@
 
 [ wxID_FOURCALC, wxID_FOURSEARCH, wxID_FOURCLEAR, wxID_PEAKSMOVE, wxID_PEAKSCLEAR, 
-    wxID_CHARGEFLIP, wxID_PEAKSUNIQUE, wxID_PEAKSDELETE,
-] = [wx.NewId() for item in range(8)]
+    wxID_CHARGEFLIP, wxID_PEAKSUNIQUE, wxID_PEAKSDELETE, wxID_PEAKSDA,
+] = [wx.NewId() for item in range(9)]
 
 [ wxID_PWDRADD, wxID_HKLFADD, wxID_DATADELETE,
@@ -614 +614 @@
         self.MapPeaksEdit.Append(id=wxID_PEAKSMOVE, kind=wx.ITEM_NORMAL,text='Move peaks', 
             help='Move selected peaks to atom list')
+        self.MapPeaksEdit.Append(id=wxID_PEAKSDA, kind=wx.ITEM_NORMAL,text='Calc dist/ang', 
+            help='Calculate distance or angle for selection')
         self.MapPeaksEdit.Append(id=wxID_PEAKSUNIQUE, kind=wx.ITEM_NORMAL,text='Unique peaks', 
-            help='Reduce map peak list to unique set')
+            help='Select unique set')
         self.MapPeaksEdit.Append(id=wxID_PEAKSDELETE, kind=wx.ITEM_NORMAL,text='Delete peaks', 
             help='Delete selected peaks')
@@ -624 +626 @@
         
     def _init_ctrls(self, parent,name=None,size=None,pos=None):
-        wx.Frame.__init__(self,parent=parent,style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX,
+        wx.Frame.__init__(self,parent=parent,
+            style=wx.DEFAULT_FRAME_STYLE | wx.FRAME_FLOAT_ON_PARENT ^ wx.CLOSE_BOX,
             size=size,pos=pos,title='GSAS-II data display')
         self._init_menus()

trunk/GSASIImath.py ¶

@@ -796 +796 @@
             Rcf = 100.
             break
+    del MEhkl,Emask,DEhkl,CErho,CEsig
     np.seterr(**old)
     print ' Charge flip time: %.4f'%(time.time()-time0),'no. elements: %d'%(Ehkl.size)
+    CErho = np.real(fft.fftn(fft.fftshift(CEhkl)))
     print ' No.cycles = ',Ncyc,'Residual Rcf =%8.3f%s'%(Rcf,'%')+' Map size:',CErho.shape
-    CErho = np.real(fft.fftn(fft.fftshift(CEhkl)))
     roll = findOffset(SGData,CEhkl)
         
@@ -821 +822 @@
         
     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]:
+        XYZ = np.inner(Amat,xyz)
+        if True in [np.allclose(XYZ,np.inner(Amat,peak),atol=0.5) for peak in peaks]:
             print ' Peak',xyz,' <0.5A from another peak'
             return False
         return True
-                        
+                            
+    def fixSpecialPos(xyz,SGData,Amat):
+        equivs = G2spc.GenAtom(xyz,SGData,Move=True)
+        X = []
+        xyzs = [equiv[0] for equiv in equivs]
+        for x in xyzs:
+            if np.sqrt(np.sum(np.inner(Amat,xyz-x)**2,axis=0))<0.5:
+                X.append(x)
+        if len(X) > 1:
+            return np.average(X,axis=0)
+        else:
+            return xyz
+        
     def findRoll(rhoMask,mapHalf):
         indx = np.array(ma.nonzero(rhoMask)).T
@@ -906 +920 @@
             if keepDup:
                 if noDuplicate(peak,peaks,Amat):
+                    peak = fixSpecialPos(peak,SGData,Amat)
                     peaks.append(peak)
                     mags.append(x1[0])
@@ -912 +927 @@
                 mags.append(x1[0])
             GoOn = Pgbar.Update(len(peaks),newmsg='%s%d'%('No. Peaks found =',len(peaks)))[0]
-            if not GoOn or len(peaks) > 300:
+            if not GoOn or len(peaks) > 500:
                 break
         rho[rMM[0]:rMP[0],rMM[1]:rMP[1],rMM[2]:rMP[2]] = peakFunc(x1,rX,rY,rZ,rhoPeak,res,SGData['SGLaue'])
@@ -919 +934 @@
 
 def PeaksUnique(data,Ind):
+
+    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]
@@ -925 +946 @@
     SGData = generalData['SGData']
     mapPeaks = data['Map Peaks']
+    Indx = {}
+    XYZ = {}
     for ind in Ind:
-        XYZ = np.array(mapPeaks[ind][1:])                        
-        Equiv = G2spc.GenAtom(XYZ,SGData,Move=True)[1:]     #remove self
-        for equiv in Equiv:                                 #special position fixer
-                Dx = XYZ-np.array(equiv[0])
-                dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
-                if dist < 0.5:
-                    print equiv[0],Dx,dist
-                    mapPeaks[ind][1:] -= Dx/2.
+        XYZ[ind] = np.array(mapPeaks[ind][1:])
+        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

trunk/GSASIIphsGUI.py ¶

@@ -45 +45 @@
 
 class SymOpDialog(wx.Dialog):
-    def __init__(self,parent,SGData,New=True):
+    def __init__(self,parent,SGData,New=True,ForceUnit=False):
         wx.Dialog.__init__(self,parent,-1,'Select symmetry operator',
             pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
@@ -51 +51 @@
         self.SGData = SGData
         self.New = New
-        self.OpSelected = [0,0,0,[0,0,0],False]
+        self.Force = ForceUnit
+        self.OpSelected = [0,0,0,[0,0,0],False,False]
         mainSizer = wx.BoxSizer(wx.VERTICAL)
+        if ForceUnit:
+            choice = ['No','Yes']
+            self.force = wx.RadioBox(panel,-1,'Force to unit cell?',choices=choice)
+            self.force.Bind(wx.EVT_RADIOBOX, self.OnOpSelect)
+            mainSizer.Add(self.force,0,wx.ALIGN_CENTER_VERTICAL)
         mainSizer.Add((5,5),0)
         if SGData['SGInv']:
@@ -124 +130 @@
         if self.New:
             self.OpSelected[4] = self.new.GetSelection()
+        if self.Force:
+            self.OpSelected[5] = self.force.GetSelection()
 
     def GetSelection(self):
@@ -1429 +1437 @@
             try:
                 if dlg.ShowModal() == wx.ID_OK:
-                    Inv,Cent,Opr,Cell,New = dlg.GetSelection()
+                    Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
                     Cell = np.array(Cell)
                     cent = SGData['SGCen'][Cent]
@@ -1965 +1973 @@
             try:
                 if dlg.ShowModal() == wx.ID_OK:
-                    Inv,Cent,Opr,Cell,New = dlg.GetSelection()
+                    Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
                     Cell = np.array(Cell)
                     cent = SGData['SGCen'][Cent]
@@ -2010 +2018 @@
             try:
                 if dlg.ShowModal() == wx.ID_OK:
-                    Inv,Cent,Opr,Cell,New = dlg.GetSelection()
+                    Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
                     Cell = np.array(Cell)
                     cent = SGData['SGCen'][Cent]
@@ -3924 +3932 @@
             Ind = MapPeaks.GetSelectedRows()
             if Ind:
-                G2mth.PeaksUnique(data,Ind)
-                FillMapPeaksGrid()
+                Ind = G2mth.PeaksUnique(data,Ind)
+                for r in range(MapPeaks.GetNumberRows()):
+                    if r in Ind:
+                        MapPeaks.SelectRow(r,addToSelected=True)
+                    else:
+                        MapPeaks.DeselectRow(r)
                 G2plt.PlotStructure(G2frame,data)
     
+    def OnPeaksDA(event):
+        #distance, angle 
+        indx = MapPeaks.GetSelectedRows()
+        if len(indx) not in [2,3]:
+            print '**** ERROR - wrong number of atoms for distance or angle calculation'
+            return
+        generalData = data['General']
+        Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])            
+        mapPeaks = data['Map Peaks']
+        xyz = []
+        for i in indx:
+            xyz.append(mapPeaks[i][1:4])
+        if len(indx) == 2:
+            print ' distance for atoms %s = %.3f'%(str(indx),G2mth.getRestDist(xyz,Amat))
+        else:
+            print ' angle for atoms %s = %.2f'%(str(indx),G2mth.getRestAngle(xyz,Amat))
+                    
+                
     def OnFourierMaps(event):
         generalData = data['General']
@@ -3992 +4022 @@
         mapData = generalData['Map']
         if len(mapData['rho']):
-            pgbar = wx.ProgressDialog('Map search','No. Peaks found =',301.0, 
+            pgbar = wx.ProgressDialog('Map search','No. Peaks found =',501.0, 
                 style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT)
             screenSize = wx.ClientDisplayRect()
@@ -4011 +4041 @@
             G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.MapPeaksMenu)
             G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksMove, id=G2gd.wxID_PEAKSMOVE)
+            G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDA, id=G2gd.wxID_PEAKSDA)
             G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksUnique, id=G2gd.wxID_PEAKSUNIQUE)
             G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDelete, id=G2gd.wxID_PEAKSDELETE)
@@ -4136 +4167 @@
             G2frame.dataFrame.SetMenuBar(G2frame.dataFrame.MapPeaksMenu)
             G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksMove, id=G2gd.wxID_PEAKSMOVE)
+            G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDA, id=G2gd.wxID_PEAKSDA)
             G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksUnique, id=G2gd.wxID_PEAKSUNIQUE)
             G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksDelete, id=G2gd.wxID_PEAKSDELETE)

trunk/GSASIIplot.py ¶

@@ -2336 +2336 @@
         [uBox[2],uBox[3]],[uBox[1],uBox[5]],[uBox[2],uBox[6]],[uBox[3],uBox[7]], 
         [uBox[4],uBox[5]],[uBox[5],uBox[6]],[uBox[6],uBox[7]],[uBox[7],uBox[4]]])
+    mD = 0.1
+    mV = np.array([[[-mD,0,0],[mD,0,0]],[[0,-mD,0],[0,mD,0]],[[0,0,-mD],[0,0,mD]]])
+    mapPeakVecs = np.inner(mV,Bmat)
+
     uColors = [Rd,Gr,Bl,Wt, Wt,Wt,Wt,Wt, Wt,Wt,Wt,Wt]
     altDown = False
@@ -2409 +2413 @@
         
     def OnMouseMove(event):
+        if event.ShiftDown():           #don't want any inadvertant moves when picking
+            return
         newxy = event.GetPosition()
         page = getSelection()
@@ -2781 +2787 @@
 
     def RenderMapPeak(x,y,z,color):
-        vecs = np.array([[[-.1/cell[0],0,0],[.1/cell[0],0,0]],
-            [[0,-.1/cell[1],0],[0,.1/cell[1],0]],
-            [[0,0,-.1/cell[2]],[0,0,.1/cell[2]]]])
         xyz = np.array([x,y,z])
         glEnable(GL_COLOR_MATERIAL)
@@ -2790 +2793 @@
         glPushMatrix()
         glBegin(GL_LINES)
-        for vec in vecs:
+        for vec in mapPeakVecs:
             glVertex3fv(vec[0]+xyz)
             glVertex3fv(vec[1]+xyz)