Changeset 1060

Timestamp:

Sep 19, 2013 4:31:46 PM (10 years ago)

Author:

vondreele

Message:

mods to MC/SA stuff - some speedup done

Location:

trunk

Files:

• GSASIImath.py (modified) (9 diffs)
• GSASIIphsGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (1 diff)

trunk/GSASIImath.py

@@ -402 +402 @@
         for tor,seq in zip(RBObj['Torsions'],RBRes['rbSeq']):
             QuatA = AVdeg2Q(tor[0],Cart[seq[0]]-Cart[seq[1]])
-            for ride in seq[3]:
-                Cart[ride] = prodQVQ(QuatA,Cart[ride]-Cart[seq[1]])+Cart[seq[1]]
+            Cart[seq[3]] = prodQVQ(Quata,(Cart[seq[3]]-Cart[seq[1]]).T).T+Cart[seq[1]]
+#            for ride in seq[3]:
+#                Cart[ride] = prodQVQ(QuatA,Cart[ride]-Cart[seq[1]])+Cart[seq[1]]
     XYZ = np.zeros_like(Cart)
     for i,xyz in enumerate(Cart):
@@ -2564 +2565 @@
                     for itor,seq in enumerate(RBRes['rbSeq']):
                         QuatA = AVdeg2Q(parmDict[pfx+'Tor'+str(itor)],Cart[seq[0]]-Cart[seq[1]])
+#                        Cart[seq[3]] = prodQVQ(QuatA,Cart[seq[3]]-Cart[seq[1]])+Cart[seq[1]]
                         for ride in seq[3]:
                             Cart[ride] = prodQVQ(QuatA,Cart[ride]-Cart[seq[1]])+Cart[seq[1]]
@@ -2741 +2743 @@
         nRef = len(refs)
         pfx = str(data['pId'])+'::PWLref:'
-        if covData['freshCOV'] and generalData['doPawley']:
+        if covData['freshCOV'] and generalData['doPawley'] and MCSA.get('newDmin',True):
             covMatrix = covData['covMatrix']
             rcov = np.zeros((nRef,nRef))        
@@ -2766 +2768 @@
             MCSA['rcov'] = rcov
             covData['freshCOV'] = False
+            MCSA['newDmin'] = False
         else:
             rcov = MCSA['rcov']
@@ -2838 +2841 @@
     q=r+ai+bj+ck
     """
-    VP = np.zeros(3)
     T2 = Q[0]*Q[1]
     T3 = Q[0]*Q[2]
@@ -2848 +2850 @@
     T9 = Q[2]*Q[3]
     T10 = -Q[3]*Q[3]
-    VP[0] = 2.*((T8+T10)*V[0]+(T6-T4)*V[1]+(T3+T7)*V[2])+V[0]
-    VP[1] = 2.*((T4+T6)*V[0]+(T5+T10)*V[1]+(T9-T2)*V[2])+V[1]
-    VP[2] = 2.*((T7-T3)*V[0]+(T2+T9)*V[1]+(T5+T8)*V[2])+V[2] 
-    return VP   
+    M = np.array([[T8+T10,T6-T4,T3+T7],[T4+T6,T5+T10,T9-T2],[T7-T3,T2+T9,T5+T8]])
+    VP = 2.*np.inner(M,V)
+    return VP+V 
     
 def Q2Mat(Q):
@@ -2878 +2879 @@
     '''
     Q = np.zeros(4)
-    d = np.sqrt(np.sum(np.array(V)**2))
+    d = nl.norm(np.array(V))
     if d:
         V /= d
@@ -2893 +2894 @@
     '''
     Q = np.zeros(4)
-    d = np.sqrt(np.sum(np.array(V)**2))
+    d = nl.norm(np.array(V))
     if d:
         V /= d
@@ -2920 +2921 @@
     V /= np.sin(A/2.)
     return A,V
+    
+def randomQ(r0,r1,r2,r3):
+    ''' create random quaternion from 4 random numbers in range (-1,1)
+    '''
+    sum = 0
+    Q = np.array(4)
+    Q[0] = r0
+    sum += Q[0]**2
+    Q[1] = np.sqrt(1.-sum)*r1
+    sum += Q[1]**2
+    Q[2] = np.sqrt(1.-sum)*r2
+    sum += Q[2]**2
+    Q[3] = np.sqrt(1.-sum)*np.where(r3<0.,-1.,1.)
+    return Q
+    
+def randomAVdeg(r0,r1,r2,r3):
+    ''' create random angle (deg),vector from 4 random number in range (-1,1)
+    '''
+    return Q2AVdeg(randomQ(r0,r1,r2,r3))
     
 def makeQuat(A,B,C):

trunk/GSASIIphsGUI.py

@@ -665 +665 @@
                     pass
                 dmin.SetValue("%.3f"%(MCSAdata['dmin']))          #reset in case of error
+                MCSAdata['newDmin'] = True
 
             def OnCycles(event):

trunk/GSASIIplot.py

@@ -2695 +2695 @@
                 mcsaTypes.append(atyp)
         mcsaBonds = FindPeaksBonds(mcsaXYZ)        
-#            mcsaXYZ,atTypes = G2mth.UpdateMCSAxyz(Bmat,MCSA)
-#            XYZeq = []
-#            for xyz in mcsaXYZ:
-#                XYZeq += G2spc.GenAtom(xyz,SGData)[0][1:]       #skip self xyz
-#            
-#            mcsaBonds = FindPeaksBonds(mcsaXYZ)        
     drawAtoms = drawingData.get('Atoms',[])
     mapData = {}