Changeset 4997

Timestamp:

Jul 16, 2021 9:21:10 AM (20 months ago)

Author:

vondreele

Message:

move imports to top of G2ctrlGUi code so debugger can find it
fix FillUnitCell? bug when incommensurate mag.
latest revision of incomm. mag. str. factor stuff

Location:

trunk

Files:

• GSASIIctrlGUI.py (modified) (2 diffs)
• GSASIImath.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (2 diffs)
• GSASIIstrMath.py (modified) (4 diffs)

trunk/GSASIIctrlGUI.py

@@ -143 +143 @@
 import glob
 import copy
+import ast
 import random as ran
 import webbrowser     # could postpone this for quicker startup
@@ -162 +163 @@
 import GSASIImath as G2mth
 import GSASIIstrMain as G2stMn
+import config_example
 if sys.version_info[0] >= 3:
     unicode = str

trunk/GSASIImath.py

@@ -1751 +1751 @@
     psin = np.sin(twopi*phase)
     pcos = np.cos(twopi*phase)
-    MmodA = Am[nxs,nxs,:,:]*pcos[:,:,:,nxs]    #cos term
-    MmodB = Bm[nxs,nxs,:,:]*psin[:,:,:,nxs]    #sin term
-    MmodA = np.sum(SGMT[nxs,:,nxs,:,:]*MmodA[:,:,:,nxs,:],axis=-1)*SGData['SpnFlp'][nxs,:,nxs,nxs]
-    MmodB = np.sum(SGMT[nxs,:,nxs,:,:]*MmodB[:,:,:,nxs,:],axis=-1)*SGData['SpnFlp'][nxs,:,nxs,nxs]
-    return MmodA,MmodB    #Ntau,Nops,Natm,Mxyz; cos & sin parts; sum matches drawn atom moments
+    MmodAR = Am[nxs,nxs,:,:]*pcos[:,:,:,nxs]    #cos term
+    MmodBR = Bm[nxs,nxs,:,:]*psin[:,:,:,nxs]    #sin term
+    MmodAR = np.sum(SGMT[nxs,:,nxs,:,:]*MmodAR[:,:,:,nxs,:],axis=-1)
+    MmodBR = np.sum(SGMT[nxs,:,nxs,:,:]*MmodBR[:,:,:,nxs,:],axis=-1)
+    MmodAI = Am[nxs,nxs,:,:]*psin[:,:,:,nxs]    #cos term
+    MmodBI = Bm[nxs,nxs,:,:]*pcos[:,:,:,nxs]    #sin term
+    MmodAI = np.sum(SGMT[nxs,:,nxs,:,:]*MmodAI[:,:,:,nxs,:],axis=-1)
+    MmodBI = np.sum(SGMT[nxs,:,nxs,:,:]*MmodBI[:,:,:,nxs,:],axis=-1)
+    return MmodAR,MmodBR,MmodAI,MmodBI    #Ntau,Nops,Natm,Mxyz; cos & sin parts; sum matches drawn atom moments
         
 def Modulation(H,HP,nWaves,Fmod,Xmod,Umod,glTau,glWt):

trunk/GSASIIphsGUI.py

@@ -8367 +8367 @@
                         atom[cx:cx+3] = Opp[key]
                         atom[cs-1] = cell
-                        atomData.append(atom[:cuij+9])  #not SS stuff
+                        atomData.append(atom[:cuij+7]+atom[-2:])  #not SS stuff
             data['Drawing']['Atoms'] = atomData
             GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind))

trunk/GSASIIplot.py

@@ -9340 +9340 @@
         
     def RenderBonds(x,y,z,Bonds,radius,color,slice=20):
+        if not len(Bonds):
+            return
         GL.glMaterialfv(GL.GL_FRONT_AND_BACK,GL.GL_DIFFUSE,color)
         GL.glPushMatrix()
@@ -9576 +9578 @@
         for i,xyz in enumerate(Atoms):
             ax,ay,az = xyz
-            RenderBonds(ax,ay,az,bondData[i],bondR,Color[i])
+            if len(bondData[i]):
+                RenderBonds(ax,ay,az,bondData[i],bondR,Color[i])
                 
     def Draw(caller='',Fade=[],NPkey=False):

trunk/GSASIIstrMath.py

@@ -1532 +1532 @@
             mXYZ = np.hstack((mXYZ,mXYZ))
 
-        MmodA,MmodB = G2mth.MagMod(glTau,mXYZ,modQ,MSSdata,SGData,SSGData)  #Ntau,Nops,Natm,Mxyz cos,sin parts sum matches drawing
+        MmodAR,MmodBR,MmodAI,MmodBI = G2mth.MagMod(glTau,mXYZ,modQ,MSSdata,SGData,SSGData)  #Ntau,Nops,Natm,Mxyz cos,sin parts sum matches drawing
         
         if not SGData['SGGray']:    #for fixed Mx,My,Mz
@@ -1612 +1612 @@
             MF = refDict['FF']['MF'][iBeg:iFin].T[Tindx].T   #Nref,Natm
             TMcorr = 0.539*(np.reshape(Tiso,Tuij.shape)*Tuij)[:,0,:]*Mdata*Fdata*MF/(2*Nops)     #Nref,Natm
-            HM = np.inner(Bmat,HP.T)                    #put into cartesian space X||H,Z||H*L;
-            Hlen = np.sqrt(np.sum(HM**2,axis=0))
-            eM = (HM/Hlen).T    # normalize  HP  Nref,hkl=Unit vectors || Q
+            HM = np.inner(Bmat,HP.T)                #put into cartesian space X||H,Z||H*L;
+            eM = (HM*refl.T[5]).T                   # normalize HP by d*    Nref,hkl=Unit vectors || Q
 
             if not SGData['SGGray']:     #correct -fixed Mx,My,Mz contribution              
@@ -1620 +1619 @@
                 fbm0 = TMcorr[:,nxs,:,nxs]*GSdata[nxs,:,:,:]*sinm[:,:,:,nxs]
 #  calc mag. structure factors; Nref,Ntau,Nops,Natm,Mxyz                            
-            fams = TMcorr[:,nxs,nxs,:,nxs]*np.array([np.where(H[3,i]!=0,(MmodA*cosm[i,nxs,:,:,nxs]+    
-                H[3,i]*MmodB*sinm[i,nxs,:,:,nxs]),0.) for i in range(mRef)])/2.          #Nref,Ntau,Nops,Natm,Mxyz
+            fams = TMcorr[:,nxs,nxs,:,nxs]*np.array([np.where(H[3,i]!=0,(
+                (MmodAR+H[3,i]*MmodBR)*cosm[i,nxs,:,:,nxs]+    
+                (-MmodAI+H[3,i]*MmodBI)*sinm[i,nxs,:,:,nxs])*SGData['SpnFlp'][nxs,:,nxs,nxs],
+                0.) for i in range(mRef)])/2.          #Nref,Ntau,Nops,Natm,Mxyz
                         
-            fbms = TMcorr[:,nxs,nxs,:,nxs]*np.array([np.where(H[3,i]!=0,(MmodA*sinm[i,nxs,:,:,nxs]+    
-                H[3,i]*MmodB*cosm[i,nxs,:,:,nxs]),0.) for i in range(mRef)])/2.          #Nref,Ntau,Nops,Natm,Mxyz
-
+            fbms = TMcorr[:,nxs,nxs,:,nxs]*np.array([np.where(H[3,i]!=0,(
+                (MmodAR+H[3,i]*MmodBR)*sinm[i,nxs,:,:,nxs]+    
+                (-MmodAI+H[3,i]*MmodBI)*cosm[i,nxs,:,:,nxs])*SGData['SpnFlp'][nxs,:,nxs,nxs],
+                0.) for i in range(mRef)])/2.          #Nref,Ntau,Nops,Natm,Mxyz
+            
             if not SGData['SGGray']:
                 fams += fam0[:,nxs,:,:,:]
@@ -1634 +1637 @@
             fbsm = np.sum(np.sum(fbms,axis=-2),axis=-2)
 # #put into cartesian space
-            facm = np.inner(fasm,uAmat.T)
+            facm = np.inner(fasm,uAmat.T)       #.T better than not
             fbcm = np.inner(fbsm,uAmat.T)
 #form e.F dot product