Changeset 165

Timestamp:

Oct 19, 2010 1:46:03 PM (12 years ago)

Author:

vondreele

Message:

patches for atom plotting & phase/histogram edits

Location:

trunk

Files:

• GSASIIphsGUI.py (modified) (7 diffs)
• GSASIIplot.py (modified) (5 diffs)
• GSASIIspc.py (modified) (2 diffs)

trunk/GSASIIphsGUI.py

@@ -453 +453 @@
         generalData = data['General']
         atomData = data['Atoms']
+        Items = [G2gd.wxID_ATOMSEDITINSERT, G2gd.wxID_ATOMSEDITDELETE, G2gd.wxID_ATOMSREFINE, 
+            G2gd.wxID_ATOMSMODIFY, G2gd.wxID_ATOMSTRANSFORM, G2gd.wxID_ATONTESTINSERT]
+        if atomData:
+            for item in Items:    
+                self.dataFrame.AtomsMenu.Enable(item,True)
+        else:
+            for item in Items:
+                self.dataFrame.AtomsMenu.Enable(item,False)            
+            
         AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
         Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",
@@ -1505 +1514 @@
                 i = atomA[0]
                 for j in IndB[0]:
-                    if j > i:
-                        if Styles[i] == 'polyhedra':
-                            atomData[i][-1].append(np.inner(Amat,Dx[j]))
-                        elif Styles[j] != 'polyhedra':
-                            atomData[i][-1].append(Dx[j]*Radii[i]/sumR[j])
-                            atomData[j][-1].append(-Dx[j]*Radii[j]/sumR[j])
+                    if Styles[i] == 'polyhedra':
+                        atomData[i][-1].append(np.inner(Amat,Dx[j]))
+                    elif Styles[j] != 'polyhedra' and j > i:
+                        atomData[i][-1].append(Dx[j]*Radii[i]/sumR[j])
+                        atomData[j][-1].append(-Dx[j]*Radii[j]/sumR[j])
 
     def DrawAtomsDelete(event):   
@@ -1756 +1764 @@
     def UpdateDData():
         UseList = data['Histograms']
+        if UseList:
+            self.dataFrame.DataMenu.Enable(G2gd.wxID_DATADELETE,True)
+        else:
+            self.dataFrame.DataMenu.Enable(G2gd.wxID_DATADELETE,False)            
         generalData = data['General']
         SGData = generalData['SGData']
@@ -1782 +1794 @@
             Obj.SetValue("%.4f"%(UseList[Indx[Obj.GetId()]]['Scale'][0]))          #reset in case of error
             
+        def OnCutoffVal(event):
+            Obj = event.GetEventObject()
+            try:
+                cutoff = float(Obj.GetValue())
+                if cutoff > 0:
+                    UseList[Indx[Obj.GetId()]]['Cutoff'] = cutoff
+            except ValueError:
+                pass
+            Obj.SetValue("%.3f"%(UseList[Indx[Obj.GetId()]]['Cutoff']))          #reset in case of error
+
         def OnSizeType(event):
             Obj = event.GetEventObject()
@@ -1849 +1871 @@
             Obj = event.GetEventObject()
             hist = Indx[Obj.GetId()]
-            UseList[hist]['MDtexture'][1][pid] = Obj.GetValue()
+            UseList[hist]['MDtexture'][1] = Obj.GetValue()
             
         def OnMDVal(event):
@@ -1922 +1944 @@
                 
             if item[:4] == 'PWDR' and UseList[item]['Show']:
+                cutoffSizer = wx.BoxSizer(wx.HORIZONTAL)
+                cutoffSizer.Add(wx.StaticText(dataDisplay,label=' Peak cutoff ratio: '),0,wx.ALIGN_CENTER_VERTICAL)
+                cutoffVal = wx.TextCtrl(dataDisplay,wx.ID_ANY,'%.3f'%(UseList[item]['Cutoff']),
+                    style=wx.TE_PROCESS_ENTER)                
+                Indx[cutoffVal.GetId()] = item
+                cutoffVal.Bind(wx.EVT_TEXT_ENTER,OnCutoffVal)
+                cutoffVal.Bind(wx.EVT_KILL_FOCUS,OnCutoffVal)
+                cutoffSizer.Add(cutoffVal,0,wx.ALIGN_CENTER_VERTICAL)
+                mainSizer.Add(cutoffSizer)
+                mainSizer.Add((0,5),0)
                 sizeSizer = wx.BoxSizer(wx.HORIZONTAL)
                 choices = ['isotropic','uniaxial',]
@@ -2142 +2174 @@
                             'Size':['isotropic',[10000.,0,],[False,False],[0,0,1]],
                             'Mustrain':['isotropic',[0.0,0,],[False,False],[0,0,1]],                            
-                            'Extinction':[0.0,False]}
+                            'Extinction':[0.0,False],'Cutoff':0.01}
                     data['Histograms'] = UseList
                     UpdateDData()

trunk/GSASIIplot.py

@@ -1126 +1126 @@
     drawingData = data['Drawing']
     drawAtoms = drawingData['Atoms']
-    Wt = [255,255,255,255]
-    Rd = [255,0,0,255]
-    Gr = [0,255,0,255]
-    Bl = [0,0,255,255]
+    Wt = [255,255,255]
+    Rd = [255,0,0]
+    Gr = [0,255,0]
+    Bl = [0,0,255]
     uBox = np.array([[0,0,0],[1,0,0],[1,1,0],[0,1,0],[0,0,1],[1,0,1],[1,1,1],[0,1,1]])
     uEdges = np.array([
@@ -1319 +1319 @@
         glBegin(GL_LINES)
         for line,color in zip(uEdges,uColors):
-            glColor4ubv(color)
+            glColor3ubv(color)
             glVertex3fv(line[0])
             glVertex3fv(line[1])
@@ -1337 +1337 @@
         glBegin(GL_LINES)
         for line,color in zip(uEdges,uColors)[:3]:
-            glColor4ubv(color)
+            glColor3ubv(color)
             glVertex3fv(line[0])
             glVertex3fv(line[1])
@@ -1390 +1390 @@
         glEnable(GL_COLOR_MATERIAL)
         glLineWidth(1)
-        glColor4fv(color)
+        glColor3fv(color)
         glPushMatrix()
         glBegin(GL_LINES)
@@ -1533 +1533 @@
                     R4 = np.concatenate((np.concatenate((R,[[0],[0],[0]]),axis=1),[[0,0,0,1],]),axis=0)
                     E = np.sqrt(E)
-                    RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)
+                    if atom[ct] == 'H' and not drawingData['showHydrogen']:
+                        pass
+                    else:
+                        RenderEllipsoid(x,y,z,ellipseProb,E,R4,color)                    
                 else:
-                    radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
-                    RenderSphere(x,y,z,radius,color)
+                    if atom[ct] == 'H' and not drawingData['showHydrogen']:
+                        pass
+                    else:
+                        radius = ellipseProb*math.sqrt(abs(atom[cs+4]))
+                        RenderSphere(x,y,z,radius,color)
             elif 'lines' in atom[cs]:
                 radius = 0.1

trunk/GSASIIspc.py

@@ -3 +3 @@
 import numpy as np
 import numpy.ma as ma
+import numpy.linalg as nl
 import math
 import sys
@@ -595 +596 @@
     return GetKNsym(str(Isym)),Mult
     
+def ElemPosition(SGData):
+    ''' Under development
+    Object here is to return a list of symmetry element types and locations suitable
+    for say drawing them.
+    So far I have the element type... getting all possible locations without lookup may be impossible!
+    '''
+    SymElements = []
+    Inv = SGData['SGInv']
+    Cen = SGData['SGCen']
+    eleSym = {-3:['','-1'],-2:['',-6],-1:['2','-4'],0:['3','-3'],1:['4','m'],2:['6',''],3:['1','']}
+    # get operators & expand if centrosymmetric
+    Ops = SGData['SGOps']
+    opM = np.array([op[0].T for op in Ops])
+    opT = np.array([op[1] for op in Ops])
+    if Inv:
+        opM = np.concatenate((opM,-opM))
+        opT = np.concatenate((opT,-opT))
+    opMT = zip(opM,opT)
+    for M,T in opMT[1:]:        #skip I
+        Dt = int(nl.det(M))
+        Tr = int(np.trace(M))
+        Dt = -(Dt-1)/2
+        Es = eleSym[Tr][Dt]
+        if Dt:              #rotation-inversion
+            I = np.eye(3)
+            if Tr == 1:     #mirrors/glides
+                if np.any(T):       #glide
+                    M2 = np.inner(M,M)
+                    MT = np.inner(M,T)+T
+                    print 'glide',Es,MT
+                    print M2
+                else:               #mirror
+                    print 'mirror',Es,T
+                    print I-M
+                X = [-1,-1,-1]
+            elif Tr == -3:  # pure inversion
+                X = np.inner(nl.inv(I-M),T)
+                print 'inversion',Es,X
+            else:           #other rotation-inversion
+                M2 = np.inner(M,M)
+                MT = np.inner(M,T)+T
+                print 'rot-inv',Es,MT
+                print M2
+                X = [-1,-1,-1]
+                
+            
+            
+        else:               #rotations
+            print 'rotation',Es
+            X = [-1,-1,-1]
+        #SymElements.append([Es,X])
+        
+    return #SymElements
+        
+        
+        
+    
+    
 def U2Uij(U):
     #returns the UIJ vector U11,U22,U33,U12,U13,U23 from tensor U