Changeset 2450

Timestamp:

Aug 25, 2016 12:22:04 PM (9 years ago)

Author:

vondreele

Message:

fix error in matrix in getCellEsd & RetDistAngle?
Add new atom drawing option for sphere of enclosure

Location:

trunk

Files:

• GSASIIgrid.py (modified) (3 diffs)
• GSASIIphsGUI.py (modified) (2 diffs)
• GSASIIstrIO.py (modified) (1 diff)
• GSASIIstrMain.py (modified) (1 diff)

trunk/GSASIIgrid.py ¶

@@ -75 +75 @@
     wxID_DRAWVIEWPOINT, wxID_DRAWTRANSFORM, wxID_DRAWDELETE, wxID_DRAWFILLCELL, 
     wxID_DRAWADDEQUIV, wxID_DRAWFILLCOORD, wxID_DRAWDISAGLTOR,  wxID_DRAWPLANE,
-    wxID_DRAWDISTVP,
-] = [wx.NewId() for item in range(13)]
+    wxID_DRAWDISTVP, wxID_DRAWADDSPHERE,
+] = [wx.NewId() for item in range(14)]
 
 [ wxID_DRAWRESTRBOND, wxID_DRAWRESTRANGLE, wxID_DRAWRESTRPLANE, wxID_DRAWRESTRCHIRAL,
@@ -324 +324 @@
         
 ################################################################################
+class SphereEnclosure(wx.Dialog):
+    ''' Add atoms within sphere of enclosure to drawing
+    
+    :param wx.Frame parent: reference to parent frame (or None)
+    :param general: general data (includes drawing data)
+    :param atoms: drawing atoms data
+    
+    '''
+    def __init__(self,parent,general,drawing,indx):
+        wx.Dialog.__init__(self,parent,wx.ID_ANY,'Setup phase transformation', 
+            pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
+        self.panel = wx.Panel(self)         #just a dummy - gets destroyed in Draw!
+        self.General = general
+        self.Drawing = drawing
+        self.indx = indx
+        self.Sphere = 1.0
+        self.centers = []
+        
+        self.Draw()
+        
+    def Draw(self):
+        
+        def OnRadius(event):
+            event.Skip()
+            try:
+                val = float(radius.GetValue())
+                if val < 0.5:
+                    raise ValueError
+                self.Sphere = val
+            except ValueError:
+                pass
+            radius.SetValue('%.3f'%(self.Sphere))
+        
+        self.panel.Destroy()
+        self.panel = wx.Panel(self)
+        mainSizer = wx.BoxSizer(wx.VERTICAL)
+        mainSizer.Add(wx.StaticText(self.panel,label=' Sphere of enclosure controls:'),0,WACV)
+        topSizer = wx.BoxSizer(wx.HORIZONTAL)
+        atoms = []
+        if len(self.indx):
+            topSizer.Add(wx.StaticText(self.panel,label=' Sphere centered at atoms: '),0,WACV)
+            cx,ct,cs = self.Drawing['atomPtrs'][:3]
+#            print self.Drawing.keys()
+            for id in self.indx:
+                atom = self.Drawing['Atoms'][id]
+                self.centers.append(atom[cx:cx+3])
+                atoms.append('%s(%s)'%(atom[ct-1],atom[cs-1]))
+            topSizer.Add(wx.ComboBox(self.panel,choices=atoms,value=atoms[0],
+                style=wx.CB_READONLY|wx.CB_DROPDOWN),0,WACV)
+        else:
+            topSizer.Add(wx.StaticText(self.panel,label=' Sphere centered at drawing view point'),0,WACV)
+            self.centers.append(self.Drawing['viewPoint'][0])
+        mainSizer.Add(topSizer,0,WACV)
+        sphereSizer = wx.BoxSizer(wx.HORIZONTAL)
+        sphereSizer.Add(wx.StaticText(self.panel,label=' Sphere radius: '),0,WACV)
+        radius = wx.TextCtrl(self.panel,value='%.3f'%(self.Sphere),style=wx.TE_PROCESS_ENTER)
+        radius.Bind(wx.EVT_TEXT_ENTER,OnRadius)
+        radius.Bind(wx.EVT_KILL_FOCUS,OnRadius)
+        sphereSizer.Add(radius,0,WACV)
+        mainSizer.Add(sphereSizer,0,WACV)
+        
+        OkBtn = wx.Button(self.panel,-1,"Ok")
+        OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
+        cancelBtn = wx.Button(self.panel,-1,"Cancel")
+        cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
+        btnSizer = wx.BoxSizer(wx.HORIZONTAL)
+        btnSizer.Add((20,20),1)
+        btnSizer.Add(OkBtn)
+        btnSizer.Add((20,20),1)
+        btnSizer.Add(cancelBtn)
+        btnSizer.Add((20,20),1)
+        
+        mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
+        self.panel.SetSizer(mainSizer)
+        self.panel.Fit()
+        self.Fit()
+        
+    def GetSelection(self):
+        return self.centers,self.Sphere
+
+    def OnOk(self,event):
+        parent = self.GetParent()
+        parent.Raise()
+        self.EndModal(wx.ID_OK)
+
+    def OnCancel(self,event):
+        parent = self.GetParent()
+        parent.Raise()
+        self.EndModal(wx.ID_CANCEL)
+        
+################################################################################
 class TransformDialog(wx.Dialog):
-    ''' Phaae transformation
+    ''' Phase transformation
     
     :param wx.Frame parent: reference to parent frame (or None)
@@ -2054 +2145 @@
         self.DrawAtomEdit.Append(id=wxID_DRAWADDEQUIV, kind=wx.ITEM_NORMAL,text='Add atoms',
             help='Add symmetry & cell equivalents to drawing set from selected atoms')
+        self.DrawAtomEdit.Append(id=wxID_DRAWADDSPHERE, kind=wx.ITEM_NORMAL,text='Add sphere of atoms',
+            help='Add atoms within sphere of enclosure')
         self.DrawAtomEdit.Append(id=wxID_DRAWTRANSFORM, kind=wx.ITEM_NORMAL,text='Transform draw atoms',
             help='Transform selected atoms by symmetry & cell translations')

trunk/GSASIIphsGUI.py ¶

@@ -4166 +4166 @@
             G2plt.PlotStructure(G2frame,data)
             
+    def AddSphere(event):
+        generalData = data['General']
+        Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
+        atomData = data['Drawing']['Atoms']
+        numAtoms = len(atomData)
+        cx,ct,cs,ci = data['Drawing']['atomPtrs']
+        cuij = cs+5
+        generalData = data['General']
+        SGData = generalData['SGData']
+        cellArray = G2lat.CellBlock(1)
+        indx = drawAtoms.GetSelectedRows()
+        indx.sort()
+        dlg = G2gd.SphereEnclosure(G2frame,data['General'],data['Drawing'],indx)
+        try:
+            if dlg.ShowModal() == wx.ID_OK:
+                centers,radius = dlg.GetSelection()
+                for orig in centers:
+                    xyzA = np.array(orig)
+                    for atomB in atomData[:numAtoms]:
+                        xyzB = np.array(atomB[cx:cx+3])
+                        Uij = atomB[cuij:cuij+6]
+#                        GSASIIpath.IPyBreak()
+                        result = G2spc.GenAtom(xyzB,SGData,False,Uij,True)
+                        for item in result:
+                            atom = copy.copy(atomB)
+                            atom[cx:cx+3] = item[0]
+                            atom[cx+3] = str(item[2])+'+'
+                            atom[cuij:cuij+6] = item[1]
+                            for xyz in cellArray+np.array(atom[cx:cx+3]):
+                                dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
+                                if 0 < dist <= radius:
+                                    if noDuplicate(xyz,atomData):
+                                        C = xyz-atom[cx:cx+3]+item[3]
+                                        newAtom = atom[:]
+                                        newAtom[cx:cx+3] = xyz
+                                        newAtom[cx+3] += str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
+                                        atomData.append(newAtom)
+        finally:
+            dlg.Destroy()
+        UpdateDrawAtoms()
+        drawAtoms.ClearSelection()
+        G2plt.PlotStructure(G2frame,data)
+            
     def TransformSymEquiv(event):
         indx = drawAtoms.GetSelectedRows()
@@ -7597 +7640 @@
         G2frame.dataFrame.Bind(wx.EVT_MENU, SetViewPoint, id=G2gd.wxID_DRAWVIEWPOINT)
         G2frame.dataFrame.Bind(wx.EVT_MENU, AddSymEquiv, id=G2gd.wxID_DRAWADDEQUIV)
+        G2frame.dataFrame.Bind(wx.EVT_MENU, AddSphere, id=G2gd.wxID_DRAWADDSPHERE)
         G2frame.dataFrame.Bind(wx.EVT_MENU, TransformSymEquiv, id=G2gd.wxID_DRAWTRANSFORM)
         G2frame.dataFrame.Bind(wx.EVT_MENU, FillCoordSphere, id=G2gd.wxID_DRAWFILLCOORD)            

trunk/GSASIIstrIO.py ¶

@@ -1487 +1487 @@
         Ax[3]*Ax[5]-Ax[1]*Ax[4],
         Ax[3]*Ax[4]-Ax[0]*Ax[5]])
-    srcvlsq = np.inner(drVdA,np.inner(vcov,drVdA.T))
+    srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov))
     Vol = 1/np.sqrt(rVsq)
     sigVol = Vol**3*np.sqrt(srcvlsq)/2.         #ok - checks with GSAS

trunk/GSASIIstrMain.py ¶

@@ -538 +538 @@
                                 sig = 0.0
                                 if len(Xvcov):
-                                    sig = np.sqrt(np.inner(pdpx,np.inner(Xvcov,pdpx)))
+                                    sig = np.sqrt(np.inner(pdpx,np.inner(pdpx,Xvcov)))
                                 Dist.append([Oatom[0],Tatom[0],tunit,Top,ma.getdata(dist[indb])[i],sig])
                                 if (Dist[-1][-2]-AsumR) <= 0.: