Changeset 2052

Timestamp:

Nov 14, 2015 4:13:43 PM (8 years ago)

Author:

vondreele

Message:

relax cell order rules for C- ortho & C-mono cell indexing
change default view of modulation plot
work on powder incommensurate fxn & derivs.

Location:

trunk

Files:

• GSASIIindex.py (modified) (2 diffs)
• GSASIImath.py (modified) (2 diffs)
• GSASIIplot.py (modified) (4 diffs)
• GSASIIstrMath.py (modified) (3 diffs)

trunk/GSASIIindex.py

@@ -146 +146 @@
     elif Bravais in [7,8,9,10]:       #orthorhombic - F,I,C,P - a<b<c convention
         abc = [ranaxis(dmin,dmax),ranaxis(dmin,dmax),ranaxis(dmin,dmax)]
-        abc.sort()
+        if Bravais in [7,8,10]:
+            abc.sort()
         a = abc[0]
         b = abc[1]
@@ -153 +154 @@
     elif Bravais in [11,12]:        #monoclinic - C,P - a<c convention
         ac = [ranaxis(dmin,dmax),ranaxis(dmin,dmax)]
-        ac.sort()
+        if Bravais == 12:
+            ac.sort()
         a = ac[0]
         b = ranaxis(dmin,dmax)

trunk/GSASIImath.py

@@ -1002 +1002 @@
     numeric = True   
     cosHA,sinHA = Modulation(waveTypes,np.array([H,]),np.array([HP,]),FSSdata,XSSdata,USSdata,Mast)
-    Mf = [H.shape[0],]+list(FSSdata.T.shape)    #ops x atoms x waves x 2 (sin+cos frac mods)
+    Mf = [H.shape[0],]+list(FSSdata.T.shape)    #=[ops,atoms,waves,2] (sin+cos frac mods)
     dGdMfC = np.zeros(Mf)
     dGdMfS = np.zeros(Mf)
-    Mx = [H.shape[0],]+list(XSSdata.T.shape)   #ops x atoms x waves x 6 (sin+cos pos mods)
+    Mx = [H.shape[0],]+list(XSSdata.T.shape)   #=[ops,atoms,waves,6] (sin+cos pos mods)
     dGdMxC = np.zeros(Mx)
     dGdMxS = np.zeros(Mx)
-    Mu = [H.shape[0],]+list(USSdata.T.shape)    #ops x atoms x waves x 12 (sin+cos Uij mods)
+    Mu = [H.shape[0],]+list(USSdata.T.shape)    #=[ops,atoms,waves,12] (sin+cos Uij mods)
     dGdMuC = np.zeros(Mu)
     dGdMuS = np.zeros(Mu)
@@ -1034 +1034 @@
             #XmodZ = 0   replace
     tauX = np.arange(1.,Ax.shape[1]+1-nx)[:,nxs]*glTau  #Xwaves x 32
-    StauX = np.ones_like(Ax)[:,nx:,:,nxs]*np.sin(twopi*tauX)[nxs,:,nxs,:]   #atoms X waves X pos X 32
+    StauX = np.ones_like(Ax)[:,nx:,:,nxs]*np.sin(twopi*tauX)[nxs,:,nxs,:]   #atoms X waves X 3(xyz) X 32
     CtauX = np.ones_like(Bx)[:,nx:,:,nxs]*np.cos(twopi*tauX)[nxs,:,nxs,:]   #ditto
     XmodA = Ax[:,nx:,:,nxs]*StauX #atoms X waves X pos X 32

trunk/GSASIIplot.py

@@ -1041 +1041 @@
     global DifLine
     global Ymax
+    global Pattern
     plottype = plotType
     if not G2frame.PatternId:
@@ -1248 +1249 @@
             Page.figure.gca().draw_artist(G2frame.itemPicked)
             Page.canvas.blit(Page.figure.gca().bbox)
+            
         def OnDragLine(event):
             '''Respond to dragging of a plot line
@@ -3124 +3126 @@
     ix = rhoSize[:3]/2
     ib = 4
-    hdx = [0,0,0]       #this needs to be something for an offset correction on atom positions
+    hdx = [2,2,2]       #this needs to be something for an offset correction on atom positions
     if Ax == 'x':
         Doff = (hdx[0]+Off)*.005
@@ -3146 +3148 @@
     else:
         Plot.contour(Slab[:,:21],20,extent=(0.,2.,-.5+Doff,.5+Doff))
+    Plot.set_ylim([-0.25,0.25])
     Page.canvas.draw()
    

trunk/GSASIIstrMath.py

@@ -1083 +1083 @@
 #        GSASIIpath.IPyBreak()
         if 'P' in calcControls[hfx+'histType']:
-            refl.T[10] = np.sum(fas**2,axis=0)+np.sum(fbs**2,axis=0)
+            refl.T[10] = np.sum(fas,axis=0)**2+np.sum(fbs,axis=0)**2    #square of sums
+#            refl.T[10] = np.sum(fas**2,axis=0)+np.sum(fbs**2,axis=0)
             refl.T[11] = atan2d(fbs[0],fas[0])  #ignore f' & f"
         else:
@@ -1265 +1266 @@
             dfbdfl = 1.0
         #NB: the above have been checked against PA(1:10,1:2) in strfctr.for for Al2O3!    
+        SA = fas[0]+fas[1]      #float = A+A' (might be array[nTwin])
+        SB = fbs[0]+fbs[1]      #float = B+B' (might be array[nTwin])
         if 'P' in calcControls[hfx+'histType']: #checked perfect for centro & noncentro
-            dFdfr[iref] = 2.*(fas[0]*dfadfr[0]+fas[1]*dfadfr[1])*Mdata/len(Uniq)+   \
-                2.*(fbs[0]*dfbdfr[0]-fbs[1]*dfbdfr[1])*Mdata/len(Uniq)
-            dFdx[iref] = 2.*(fas[0]*dfadx[0]+fas[1]*dfadx[1])+  \
-                2.*(fbs[0]*dfbdx[0]+fbs[1]*dfbdx[1])
-            dFdui[iref] = 2.*(fas[0]*dfadui[0]+fas[1]*dfadui[1])+   \
-                2.*(fbs[0]*dfbdui[0]-fbs[1]*dfbdui[1])
-            dFdua[iref] = 2.*(fas[0]*dfadua[0]+fas[1]*dfadua[1])+   \
-                2.*(fbs[0]*dfbdua[0]+fbs[1]*dfbdua[1])
-            dFdGx[iref] = 2.*(fas[0]*dfadGx[0]+fas[1]*dfadGx[1])+  \
-                2.*(fbs[0]*dfbdGx[0]+fbs[1]*dfbdGx[1])
-            dFdGu[iref] = 2.*(fas[0]*dfadGu[0]+fas[1]*dfadGu[1])+  \
-                2.*(fbs[0]*dfbdGu[0]+fbs[1]*dfbdGu[1])
+            dFdfr[iref] = 2.*(SA*dfadfr[0]+SA*dfadfr[1]+SB*dfbdfr[0]+SB*dfbdfr[1])*Mdata/len(Uniq) #array(nRef,nAtom)
+            dFdx[iref] = 2.*(SA*dfadx[0]+SA*dfadx[1]+SB*dfbdx[0]+SB*dfbdx[1])    #array(nRef,nAtom,3)
+            dFdui[iref] = 2.*(SA*dfadui[0]+SA*dfadui[1]+SB*dfbdui[0]+SB*dfbdui[1])   #array(nRef,nAtom)
+            dFdua[iref] = 2.*(SA*dfadua[0]+SA*dfadua[1]+SB*dfbdua[0]+SB*dfbdua[1])    #array(nRef,nAtom,6)
+            dFdfl[iref] = -SA*dfadfl-SB*dfbdfl                  #array(nRef,) 
+                           
+            dFdGf[iref] = 2.*(SA*dfadGf[0]+SB*dfbdGf[1])      #array(nRef,natom,nwave,2)
+            dFdGx[iref] = 2.*(SA*dfadGx[0]+SB*dfbdGx[1])      #array(nRef,natom,nwave,6)
+            dFdGu[iref] = 2.*(SA*dfadGu[0]+SB*dfbdGu[1])      #array(nRef,natom,nwave,12)
+#            dFdfr[iref] = 2.*(fas[0]*dfadfr[0]+fas[1]*dfadfr[1])*Mdata/len(Uniq)+   \
+#                2.*(fbs[0]*dfbdfr[0]-fbs[1]*dfbdfr[1])*Mdata/len(Uniq)
+#            dFdx[iref] = 2.*(fas[0]*dfadx[0]+fas[1]*dfadx[1])+  \
+#                2.*(fbs[0]*dfbdx[0]+fbs[1]*dfbdx[1])
+#            dFdui[iref] = 2.*(fas[0]*dfadui[0]+fas[1]*dfadui[1])+   \
+#                2.*(fbs[0]*dfbdui[0]-fbs[1]*dfbdui[1])
+#            dFdua[iref] = 2.*(fas[0]*dfadua[0]+fas[1]*dfadua[1])+   \
+#                2.*(fbs[0]*dfbdua[0]+fbs[1]*dfbdua[1])
+#            dFdGf[iref] = 2.*(fas[0]*dfadGf[0]+fas[1]*dfadGf[1])+  \
+#                2.*(fbs[0]*dfbdGf[0]+fbs[1]*dfbdGf[1])
+#            dFdGx[iref] = 2.*(fas[0]*dfadGx[0]+fas[1]*dfadGx[1])+  \
+#                2.*(fbs[0]*dfbdGx[0]+fbs[1]*dfbdGx[1])
+#            dFdGu[iref] = 2.*(fas[0]*dfadGu[0]+fas[1]*dfadGu[1])+  \
+#                2.*(fbs[0]*dfbdGu[0]+fbs[1]*dfbdGu[1])
         else:
-            SA = fas[0]+fas[1]      #float = A+A' (might be array[nTwin])
-            SB = fbs[0]+fbs[1]      #float = B+B' (might be array[nTwin])
             if nTwin > 1:
                 dFdfr[iref] = [2.*TwMask[it]*(SA[it]*dfadfr[0][it]+SA[it]*dfadfr[1][it]+SB[it]*dfbdfr[0][it]+SB[it]*dfbdfr[1][it])*Mdata/len(Uniq[it]) for it in range(nTwin)]
@@ -2624 +2636 @@
                         try:
                             aname = name.split(pfx)[1][:2]
-                            if aname not in ['Af','dA','AU','RB']: continue # skip anything not an atom or rigid body param
+                            if aname not in ['Af','dA','AU','RB','Xs','Xc','Ys','Yc','Zs','Zc','U1','U2','U3']: continue # skip anything not an atom or rigid body param
                         except IndexError:
                             continue