Changeset 2184

Timestamp:

Mar 25, 2016 10:36:47 AM (8 years ago)

Author:

vondreele

Message:

fix problems in adding atoms, etc for 'faulted' phases in the regular phase stuff

Location:

trunk

Files:

• GSASIIimgGUI.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (10 diffs)
• GSASIIpwd.py (modified) (1 diff)
• GSASIIstrIO.py (modified) (1 diff)

trunk/GSASIIimgGUI.py

@@ -362 +362 @@
             
 # Sizers
-                                        
+    Indx = {}                                    
     def ComboSizer():
 
@@ -525 +525 @@
             'phi':['Tilt rotation','%.2f',data['rotation']],'dep':['Penetration','%.2f',data['DetDepth']],
             'wave':['Wavelength','%.6f',data['wavelength']]}
-        Indx = {}
+#        Indx = {}
         for name in Names:
             calSel = wx.CheckBox(parent=G2frame.dataDisplay,label=Parms[name][0])

trunk/GSASIIphsGUI.py

@@ -1205 +1205 @@
         
         mainSizer.Add(FlipSizer())
-        if generalData['Type'] in ['nuclear','macromolecular']:
+        if generalData['Type'] in ['nuclear','macromolecular','faulted',]:
             G2G.HorizontalLine(mainSizer,General)
             mainSizer.Add(MCSASizer())
@@ -1249 +1249 @@
                 if Atoms.GetColLabelValue(c) == 'refine':
                     Type = generalData['Type']
-                    if Type in ['nuclear','macromolecular','modulated']:
+                    if Type in ['nuclear','macromolecular','modulated','faulted',]:
                         choice = ['F - site fraction','X - coordinates','U - thermal parameters']
                     elif Type in ['magnetic',]:
@@ -1669 +1669 @@
         if generalData['Type'] == 'macromolecular':
             atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
-        elif generalData['Type'] == 'nuclear':
+        elif generalData['Type'] in ['nuclear','faulted',]:
             atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
-        elif generalData['Type'] in ['modulated','magnetic']:
+        elif generalData['Type'] in ['modulated','magnetic',]:
             atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId,[],[],
                 {'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}])
@@ -1853 +1853 @@
         generalData = data['General']
         SGData = generalData['SGData']
-        if generalData['Type'] in ['nuclear','modulated',]:
+        if generalData['Type'] in ['nuclear','modulated','faulted',]:
             if oldatom:
                 opr = oldatom[5]
@@ -1888 +1888 @@
         if generalData['Type'] == 'macromolecular':
             atomData.insert(indx,[0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
-        elif generalData['Type'] == 'nuclear':
+        elif generalData['Type'] in ['nuclear','faulted',]:
             atomData.insert(indx,[Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
         elif generalData['Type'] in ['modulated','magnetic']:
@@ -2411 +2411 @@
         plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],
             'viewPoint':[[0.,0.,0.],[]],}
+        Indx = {}
 
         def OnLaue(event):
@@ -2526 +2527 @@
             widths = Layers['Width'][0]
             flags = Layers['Width'][1]
-            Indx = {}
             widthSizer = wx.BoxSizer(wx.HORIZONTAL)
             for i in range(2):
@@ -2664 +2664 @@
             Names = [layer['Name'] for layer in Layers['Layers']]
             transArray = Layers['Transitions']
-            Indx = {}
             layerData.transGrids = []
             if not Names or not transArray:
@@ -3272 +3271 @@
             drawingData['showRigidBodies'] = True
         cx,ct,cs,ci = [0,0,0,0]
-        if generalData['Type'] in ['nuclear','modulated']:
+        if generalData['Type'] in ['nuclear','modulated','faulted',]:
             cx,ct,cs,ci = [2,1,6,17]         #x, type, style & index
         elif generalData['Type'] == 'macromolecular':
@@ -4315 +4314 @@
         SetupDrawingData()
         drawingData = data['Drawing']
-        if generalData['Type'] == 'nuclear':
+        if generalData['Type'] in ['nuclear','faulted',]:
             pickChoice = ['Atoms','Bonds','Torsions','Planes']
         elif generalData['Type'] == 'macromolecular':

trunk/GSASIIpwd.py

@@ -1936 +1936 @@
 def CalcStackingSADP(Layers):
     
-    def getXY_HK(hk,Layers):
-        XY_HK = {}
-        for layer in Layers['Layers']:
-            if not layer['SameAs']:     #a real layer
-                XY_HK[layer['Name']] = np.inner(hk,np.array([atom[2:4] for atom in layer['Atoms']]))*2.*np.pi
-        return XY_HK
+    atTypes = Layers['AtInfo'].keys()
+    Adat = []
+    for atType in atTypes:
+        if atType == 'H': 
+            blen = -.3741
+        else:
+            blen = Layers['AtInfo'][atType]['Isotopes']['Nat. Abund.']['SL'][0]
+        Adat.append([[Adat['fa'][i],Adat['fb'][i]] for i in range(4)]+[Adat['fc'],])
+    Adat = np.array(Adat).flatten()
+    AtomXOU = []
+    AtomTp = []
+    AtomNL = []
+    LayerSymm = []
+    LayerNum = []
+    layerNames = []
+    Natm = 1
+    Nuniq = 0
+    for layer in Layers['Layers']:
+        layerNames.append(layer['Name'])
+    for il,layer in enumerate(Layers['Layers']):
+        if layer['SameAs']:
+            LayerNum.append(layerNames.index(layer['SameAs'])+1)
+            continue
+        else:
+            LayerNum.append(il)
+            Nuniq += 1
+        if '-1' in layer['Symm']:
+            LayerSymm.append(1)
+        else:
+            LayerSymm.append(0)
+        AtomNL.append(Natm)
+        for ia,atom in enumerate(layer['Atoms']):
+            [name,atype,x,y,z,frac,Uiso] = atom
+            Natm += 1
+            AtomTp.append(atype)
+            AtomXOU.append([x,y,z,frac,Uiso*78.9568])
+    TransX = []
+    TransP = []
+    for Ytrans in Layers['Transitions']:
+        TransP.append([trans[0] for trans in Ytrans])   #get just the numbers
+        TransX.append([trans[1:4] for trans in Ytrans])   #get just the numbers
+    TransP = np.array(Trans,dtype='float')
+    TransX = np.array(Trans,dtype='float')
+    Nlayers = np.sqrt(TransP.shape[0])
+    Cell = Layers['Cell'][1:4]+Layers['Cell'][6:7]
         
-    def getDXY_HK(hk,Trans,detune):
-        N = Trans.shape[0]
-        DXY_HK = np.zeros((N,N),dtype='cfloat')
-        Lphi = np.zeros((N,N),dtype='cfloat')
-        for iY in range(N):
-            for iX in range(N):
-                if [str(iY+1),str(iX+1)] in Layers['allowedTrans']:
-                    dot = 2.*np.pi*np.inner(hk,Trans[iY,iX,1:3])
-                    Lphi[iY,iX] = complex(np.cos(dot),np.sin(dot))
-                    DXY_HK[iY][iX] = detune*Trans[iY,iX,0]*Lphi[iY,iX]
-        return DXY_HK,Lphi
-                    
-                    
-    
-    sadpSize = 256
-    G,g = G2lat.cell2Gmat(Layers['Cell'][1:7])  #recip/real met. tensors
-    A = G2lat.Gmat2A(G)
+    laueId = ['-1','2/m(ab)','2/m(c)','mmm','-3','-3m','4/m','4/mmm',
+        '6/m','6/mmm','axial','unknown'].index(Layers['Laue'])
+    planeId = ['h0l','0kl','hhl','h-hl'],index(Layers['Sadp']['Plane'])+1
     lmax = float(Layers['Sadp']['Lmax'])
-    Smax = G2lat.calc_rDsq([0.,0.,lmax],A)
-    plane = Layers['Sadp']['Plane']
-    if plane == 'h0l':
-        hkmax = int(lmax*np.sqrt(A[2]/A[0]))
-    elif plane == '0kl':
-        hkmax = int(lmax*np.sqrt(A[2]/A[1]))
-    elif plane == 'hhl':
-        hkmax = int(lmax*np.sqrt(A[2]/(A[0]+A[1]+A[5])))
-    elif plane == 'h-hl':
-        hkmax = int(lmax*np.sqrt(A[2]/(A[0]+A[1]-A[5])))
-    dl = 2.*lmax/sadpSize
-    Trans = []
-    for Ytrans in Layers['Transitions']:
-        Trans.append([trans[:4] for trans in Ytrans])   #get just the numbers
-    Trans = np.array(Trans,dtype='float')
-    N = np.sqrt(Trans.shape[0])
-    lmax -= 0.5*dl  #shift lmax to avoid l=0
-    lmin = -lmax
-    sadpBlock = sadpSize
-    if Layers['Laue'] not in ['-1','2/m(c)','-3','-3m','axial']:
-        lmin = -0.5*dl
-        sadpBlock /= 2
-#start
-    cnt = 0
-    Names = [layer['Name'] for layer in Layers['Layers']]
-    Nlayers = len(Names)
-    detune = 1.0-0.001
-    for i in range(hkmax+1):
-        if plane == 'h0l':
-            hk = np.array([i,0])
-        elif plane == '0kl':
-            hk = np.array([0,i])
-        elif lane == 'hhl':
-            hk = np.array([i,i])
-        else:
-            hk = np.array([i,-i])
-        print ' h = %d k = %d'%(hk[0],hk[1])
-        XY_HK = getXY_HK(hk,Layers)                 #good
-        DXY_HK,Lphi = getDXY_HK(hk,Trans,detune)    #good
-             
+    controls = [laueId,planeId,lmax,Nuniq,]
         
-        
-    
+    Sadp = np.array(256**2)    
+    Sadp = pygetsadp(controls,len(AtTypes),AtTypes,Adat,Cell,Natm,AtomTp,AtomXOU,Nlayers,TransP,TransX,stackseq,Sadp)
     
     

trunk/GSASIIstrIO.py

@@ -889 +889 @@
             line = ' res no residue chain'+line
         print >>pFile,line
-        if General['Type'] in ['nuclear','modulated','magnetic']:
+        if General['Type'] in ['nuclear','modulated','magnetic','faulted',]:
             print >>pFile,135*'-'
             for i,at in enumerate(Atoms):