Changeset 2061

Timestamp:

Nov 19, 2015 9:15:05 AM (6 years ago)

Author:

vondreele

Message:

modify export app peak lists to include d-spacing as a column
fix 2x error in U2Uij & Uij2U in G2spc - now same as one in G2lat
fix math errors for Uij modulation derivatives - all ok now

Location:

trunk

Files:

• GSASII.py (modified) (1 diff)
• GSASIImath.py (modified) (5 diffs)
• GSASIIspc.py (modified) (1 diff)
• GSASIIstrMath.py (modified) (1 diff)

trunk/GSASII.py

@@ -3139 +3139 @@
                             file.write('#wavelength = %10.6f\n'%(wave))
                         if 'T' in Type:
-                            file.write('#%10s %12s %10s %10s %10s %10s %10s\n'%('pos','int','alp','bet','sig','gam','FWHM'))                                    
+                            file.write('#%9s %10s %12s %10s %10s %10s %10s %10s\n'%('pos','dsp','int','alp','bet','sig','gam','FWHM'))                                    
                         else:
-                            file.write('#%10s %12s %10s %10s %10s\n'%('pos','int','sig','gam','FWHM'))
+                            file.write('#%9s %10s %12s %10s %10s %10s\n'%('pos','dsp','int','sig','gam','FWHM'))
                         for peak in peaks:
+                            dsp = G2lat.Pos2dsp(Inst,peak[0])
                             if 'T' in Type:  #TOF - more cols
                                 FWHM = 2.*G2pwd.getgamFW(peak[10],peak[8])      #to get delta-TOF from Gam(peak)
-                                file.write("%10.5f %12.2f %10.3f %10.3f %10.3f %10.3f %10.3f\n" % \
-                                    (peak[0],peak[2],np.sqrt(max(0.0001,peak[4])),peak[6],peak[8],peak[10],FWHM))
+                                file.write("%10.2f %10.5f %12.2f %10.3f %10.3f %10.3f %10.3f %10.3f\n" % \
+                                    (peak[0],dsp,peak[2],np.sqrt(max(0.0001,peak[4])),peak[6],peak[8],peak[10],FWHM))
                             else:               #CW
                                 FWHM = 2.*G2pwd.getgamFW(peak[6],peak[4])      #to get delta-2-theta in deg. from Gam(peak)
-                                file.write("%10.5f %12.2f %10.5f %10.5f %10.5f \n" % \
-                                    (peak[0],peak[2],np.sqrt(max(0.0001,peak[4]))/100.,peak[6]/100.,FWHM/100.)) #convert to deg
+                                file.write("%10.3f %10.5f %12.2f %10.5f %10.5f %10.5f \n" % \
+                                    (peak[0],dsp,peak[2],np.sqrt(max(0.0001,peak[4]))/100.,peak[6]/100.,FWHM/100.)) #convert to deg
                     item, cookie = self.PatternTree.GetNextChild(self.root, cookie)                            
                 file.close()

trunk/GSASIImath.py

@@ -980 +980 @@
     else:
         HbH = 1.0
-    D = twopi*H[:,:,3:]*glTau[nxs,nxs,:]              #m*e*tau; refBlk x ops X 32
-    HdotX = twopi*np.inner(HP,Xmod)                   #refBlk x ops x atoms X 32
-    HdotXD = HdotX+D[:,:,nxs,:]
+    D = H[:,:,3:]*glTau[nxs,nxs,:]              #m*e*tau; refBlk x ops X 32
+    HdotX = np.inner(HP,Xmod)                   #refBlk x ops x atoms X 32
+    HdotXD = twopi*(HdotX+D[:,:,nxs,:])
     cosHA = np.sum(Fmod*HbH*np.cos(HdotXD)*glWt,axis=-1)       #real part; refBlk X ops x atoms; sum for G-L integration
     sinHA = np.sum(Fmod*HbH*np.sin(HdotXD)*glWt,axis=-1)       #imag part; ditto
@@ -993 +993 @@
     HP: array nRefBlk x ops X hklt proj to hkl
     FSSdata: array 2 x atoms x waves    (sin,cos terms)
-    Hij: array 3x3
+    Hij: array 2pi^2[a*^2h^2 b*^2k^2 c*^2l^2 a*b*hk a*c*hl b*c*kl] of projected hklm to hkl space
     XSSdata: array 2x3 x atoms X waves (sin,cos terms)
     USSdata: array 2x6 x atoms X waves (sin,cos terms)
@@ -1043 +1043 @@
     HdotX = twopi*np.inner(HP,Xmod)        #ops x atoms X 32
     HdotXD = HdotX+D[:,nxs,:]
-#    HdotXA = twopi*HP[:,nxs,nxs,nxs,:]*np.swapaxes(XmodA,-1,-2)[nxs,:,:,:,:]+D[:,nxs,nxs,:,nxs]  #ops x atoms x waves x 32 x xyz
-#    HdotXB = twopi*HP[:,nxs,nxs,nxs,:]*np.swapaxes(XmodB,-1,-2)[nxs,:,:,:,:]+D[:,nxs,nxs,:,nxs]
     if Af.shape[1]:
         tauF = np.arange(1.,Af.shape[1]+1-nf)[:,nxs]*glTau  #Fwaves x 32
@@ -1056 +1054 @@
     if Au.shape[1]:
         tauU = np.arange(1.,Au.shape[1]+1)[:,nxs]*glTau     #Uwaves x 32
-        StauU = np.ones_like(Au)[:,:,:,:,nxs]*np.sin(twopi*tauU)[nxs,:,nxs,nxs,:]   #also dUmod/dAu
-        CtauU = np.ones_like(Bu)[:,:,:,:,nxs]*np.cos(twopi*tauU)[nxs,:,nxs,nxs,:]   #also dUmod/dBu
+        StauU = np.ones_like(Au)[:,:,:,:,nxs]*np.sin(twopi*tauU)[nxs,:,nxs,nxs,:]   #also dUmodA/dAu
+        CtauU = np.ones_like(Bu)[:,:,:,:,nxs]*np.cos(twopi*tauU)[nxs,:,nxs,nxs,:]   #also dUmodB/dBu
         UmodA = Au[:,:,:,:,nxs]*StauU #atoms x waves x 3x3 x 32
         UmodB = Bu[:,:,:,:,nxs]*CtauU #ditto
         Umod = np.swapaxes((UmodA+UmodB),2,4)      #atoms x waves x 32 x 3x3 (symmetric so I can do this!) 
         HuH = np.sum(HP[:,nxs,nxs,nxs]*np.inner(HP,Umod),axis=-1)    #ops x atoms x waves x 32
-        HbH = np.exp(-np.sum(HuH,axis=-2)) # ops x atoms x 32; sum waves
+        HbH = np.exp(-np.sum(HuH,axis=-2)) # ops x atoms x 32; sum waves - OK vs Modulation version
 #derivs need to be ops x atoms x waves x 6uij; ops x atoms x waves x 32 x 6uij before sum
         StauU = np.rollaxis(np.rollaxis(np.swapaxes(StauU,2,4),-1),-1)
         CtauU = np.rollaxis(np.rollaxis(np.swapaxes(CtauU,2,4),-1),-1)
-        dUdAu = Hij[:,nxs,nxs,nxs,:]*np.rollaxis(G2lat.UijtoU6(StauU),0,4)[nxs,:,:,:,:]    #ops x atoms x waves x 32 x 6Uij
-        dUdBu = Hij[:,nxs,nxs,nxs,:]*np.rollaxis(G2lat.UijtoU6(CtauU),0,4)[nxs,:,:,:,:]    #ops x atoms x waves x 32 x 6Uij
-        part1 = -HuH*np.exp(-HuH)*Fmod[:,:,nxs,:]    #ops x atoms x waves x 32
+        dUdAu = Hij[:,nxs,nxs,nxs,:]*np.rollaxis(G2lat.UijtoU6(StauU),0,4)[nxs,:,:,:,:]    #ops x atoms x waves x 32 x 6sinUij
+        dUdBu = Hij[:,nxs,nxs,nxs,:]*np.rollaxis(G2lat.UijtoU6(CtauU),0,4)[nxs,:,:,:,:]    #ops x atoms x waves x 32 x 6cosUij
+        part1 = -np.exp(-HuH)*Fmod[:,:,nxs,:]    #ops x atoms x waves x 32
         dGdMuCa = np.sum(part1[:,:,:,:,nxs]*dUdAu*np.cos(HdotXD)[:,:,nxs,:,nxs]*glWt[nxs,nxs,nxs,:,nxs],axis=-2)   #ops x atoms x waves x 6uij; G-L sum
         dGdMuCb = np.sum(part1[:,:,:,:,nxs]*dUdBu*np.cos(HdotXD)[:,:,nxs,:,nxs]*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
-        dGdMuC = np.concatenate((dGdMuCa,dGdMuCb),axis=-1)   #ops x atoms x waves x 12uij; G-L sum
+        dGdMuC = np.concatenate((dGdMuCa,dGdMuCb),axis=-1)   #ops x atoms x waves x 12uij
         dGdMuSa = np.sum(part1[:,:,:,:,nxs]*dUdAu*np.sin(HdotXD)[:,:,nxs,:,nxs]*glWt[nxs,nxs,nxs,:,nxs],axis=-2)   #ops x atoms x waves x 6uij; G-L sum
         dGdMuSb = np.sum(part1[:,:,:,:,nxs]*dUdBu*np.sin(HdotXD)[:,:,nxs,:,nxs]*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
-        dGdMuS = np.concatenate((dGdMuSa,dGdMuSb),axis=-1)   #ops x atoms x waves x 12uij; G-L sum
+        dGdMuS = np.concatenate((dGdMuSa,dGdMuSb),axis=-1)   #ops x atoms x waves x 12uij
+#        #GSASIIpath.IPyBreak()
     else:
         HbH = np.ones_like(HdotX)
@@ -1082 +1081 @@
     dGdMxCb = -np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(dHdXB*np.sin(HdotXD)[:,:,nxs,:,nxs])*glWt[nxs,nxs,nxs,:,nxs],axis=-2)
     dGdMxC = np.concatenate((dGdMxCa,dGdMxCb),axis=-1)
-# ops x atoms x waves x 2xyz - real part
+# ops x atoms x waves x 2xyz - real part - good
     dGdMxSa = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(dHdXA*np.cos(HdotXD)[:,:,nxs,:,nxs])*glWt[nxs,nxs,nxs,:,nxs],axis=-2)    
     dGdMxSb = np.sum((Fmod*HbH)[:,:,nxs,:,nxs]*(dHdXB*np.cos(HdotXD)[:,:,nxs,:,nxs])*glWt[nxs,nxs,nxs,:,nxs],axis=-2)    
     dGdMxS = np.concatenate((dGdMxSa,dGdMxSb),axis=-1)
-# ops x atoms x waves x 2xyz - imaginary part
+# ops x atoms x waves x 2xyz - imaginary part - good
     return np.array([cosHA,sinHA]),[dGdMfC,dGdMfS],[dGdMxC,dGdMxS],[dGdMuC,dGdMuS]
     

trunk/GSASIIspc.py

@@ -2170 +2170 @@
 def U2Uij(U):
     #returns the UIJ vector U11,U22,U33,U12,U13,U23 from tensor U
-    return [U[0][0],U[1][1],U[2][2],2.*U[0][1],2.*U[0][2],2.*U[1][2]]
+    return [U[0][0],U[1][1],U[2][2],U[0][1],U[0][2],U[1][2]]
     
 def Uij2U(Uij):
     #returns the thermal motion tensor U from Uij as numpy array
-    return np.array([[Uij[0],Uij[3]/2.,Uij[4]/2.],[Uij[3]/2.,Uij[1],Uij[5]/2.],[Uij[4]/2.,Uij[5]/2.,Uij[2]]])
+    return np.array([[Uij[0],Uij[3],Uij[4]],[Uij[3],Uij[1],Uij[5]],[Uij[4],Uij[5],Uij[2]]])
 
 def StandardizeSpcName(spcgroup):

trunk/GSASIIstrMath.py

@@ -1345 +1345 @@
             dFdvDict[pfx+'U22sin:'+str(i)+':'+str(j)] = dFdGu.T[1][j][i]
             dFdvDict[pfx+'U33sin:'+str(i)+':'+str(j)] = dFdGu.T[2][j][i]
-            dFdvDict[pfx+'U12sin:'+str(i)+':'+str(j)] = dFdGu.T[3][j][i]
-            dFdvDict[pfx+'U13sin:'+str(i)+':'+str(j)] = dFdGu.T[4][j][i]
-            dFdvDict[pfx+'U23sin:'+str(i)+':'+str(j)] = dFdGu.T[5][j][i]
+            dFdvDict[pfx+'U12sin:'+str(i)+':'+str(j)] = 2.*dFdGu.T[3][j][i]
+            dFdvDict[pfx+'U13sin:'+str(i)+':'+str(j)] = 2.*dFdGu.T[4][j][i]
+            dFdvDict[pfx+'U23sin:'+str(i)+':'+str(j)] = 2.*dFdGu.T[5][j][i]
             dFdvDict[pfx+'U11cos:'+str(i)+':'+str(j)] = dFdGu.T[6][j][i]
             dFdvDict[pfx+'U22cos:'+str(i)+':'+str(j)] = dFdGu.T[7][j][i]
             dFdvDict[pfx+'U33cos:'+str(i)+':'+str(j)] = dFdGu.T[8][j][i]
-            dFdvDict[pfx+'U12cos:'+str(i)+':'+str(j)] = dFdGu.T[9][j][i]
-            dFdvDict[pfx+'U13cos:'+str(i)+':'+str(j)] = dFdGu.T[10][j][i]
-            dFdvDict[pfx+'U23cos:'+str(i)+':'+str(j)] = dFdGu.T[11][j][i]
+            dFdvDict[pfx+'U12cos:'+str(i)+':'+str(j)] = 2.*dFdGu.T[9][j][i]
+            dFdvDict[pfx+'U13cos:'+str(i)+':'+str(j)] = 2.*dFdGu.T[10][j][i]
+            dFdvDict[pfx+'U23cos:'+str(i)+':'+str(j)] = 2.*dFdGu.T[11][j][i]
             
     dFdvDict[phfx+'BabA'] = dFdbab.T[0]