Changeset 3340

Timestamp:

Apr 11, 2018 1:32:49 PM (5 years ago)

Author:

vondreele

Message:

make testDeriv py3 compatible
fix problem with Reload draw atoms - mag moments
add |Mag| to lst output of magnetic moments
correct errors in mag moment structure factor & derivatives

Location:

trunk

Files:

• GSASIIdataGUI.py (modified) (1 diff)
• GSASIIspc.py (modified) (1 diff)
• GSASIIstrIO.py (modified) (3 diffs)
• GSASIIstrMath.py (modified) (9 diffs)
• testDeriv.py (modified) (3 diffs)

trunk/GSASIIdataGUI.py

@@ -4306 +4306 @@
             return
         dlg = wx.ProgressDialog('Residual','All data Rw =',101.0, 
-            style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT|wx.STAY_ON_TOP,
-            parent=self)
+            style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT|wx.STAY_ON_TOP,parent=self)
         Size = dlg.GetSize()
         if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0

trunk/GSASIIspc.py

@@ -3186 +3186 @@
         newMom = -(np.inner(Mom,M).T)*nl.det(M)
     else:
-        newMom = -(np.inner(Mom,M).T)*SGData['SpnFlp'][nA-1]*nl.det(M)
+        newMom = -(np.inner(Mom,M).T)*SGData['MagMom'][nA-1]*nl.det(M)
     return newMom
         

trunk/GSASIIstrIO.py

@@ -1656 +1656 @@
             
     def PrintMomentsAndSig(General,Atoms,atomsSig):
+        cell = General['Cell'][1:7]
+        G = G2lat.fillgmat(cell)
+        ast = np.sqrt(np.diag(G))
+        GS = G/np.outer(ast,ast)
         pFile.write('\n Magnetic Moments:\n')    #add magnitude & angle, etc.? TBD
-        line = '   name      Mx        My        Mz'
+        line = '   name       Mx        My        Mz       |Mag|'
         cx,ct,cs,cia = General['AtomPtrs']
         cmx = cx+4
@@ -1663 +1667 @@
         pFile.write(line+'\n')
         pFile.write(135*'-'+'\n')
-        fmt = {0:'%7s',ct:'%7s',cmx:'%10.5f',cmx+1:'%10.5f',cmx+2:'%10.5f'}
+        fmt = {0:'%7s',ct:'%7s',cmx:'%10.3f',cmx+1:'%10.3f',cmx+2:'%10.3f'}
         noFXsig = {cmx:[10*' ','%10s'],cmx+1:[10*' ','%10s'],cmx+2:[10*' ','%10s']}
         for i,at in enumerate(Atoms):
@@ -1677 +1681 @@
                     else:
                         sigstr += noFXsig[ind][1]%(noFXsig[ind][0])
+                mag = np.array(at[cmx:cmx+3])
+                Mag = np.sqrt(np.inner(mag,np.inner(mag,GS)))
+                valstr += '%10.3f'%Mag
+                sigstr += 10*' '
                 pFile.write(name+'\n')
                 pFile.write(valstr+'\n')

trunk/GSASIIstrMath.py

@@ -786 +786 @@
 
     '''        
-#    phfx = pfx.split(':')[0]+hfx
     ast = np.sqrt(np.diag(G))
     GS = G/np.outer(ast,ast)
+    uAmat = G2lat.Gmat2AB(GS)[0]
     Mast = twopisq*np.multiply.outer(ast,ast)
     SGMT = np.array([ops[0].T for ops in SGData['SGOps']])
@@ -797 +797 @@
         Nops *= (1+SGData['SGInv'])
     MFtables = calcControls['MFtables']
-    Amat,Bmat = G2lat.Gmat2AB(G)
+    Bmat = G2lat.Gmat2AB(G)[1]
     TwinLaw = np.ones(1)
 #    TwinLaw = np.array([[[1,0,0],[0,1,0],[0,0,1]],])
@@ -812 +812 @@
         return
     Mag = np.sqrt(np.array([np.inner(mag,np.inner(mag,GS)) for mag in Gdata.T]))
-    Gdata = np.where(Mag>0.,Gdata/Mag,0.)       #normalze mag. moments
     Gdata = np.inner(Gdata.T,SGMT).T            #apply sym. ops.
     if SGData['SGInv'] and not SGData['SGFixed']:
         Gdata = np.hstack((Gdata,-Gdata))       #inversion if any
-    Gdata = np.hstack([Gdata for icen in range(Ncen)])        #dup over cell centering
+    Gdata = np.hstack([Gdata for icen in range(Ncen)])        #dup over cell centering--> [Mxyz,nops,natms]
     Gdata = SGData['MagMom'][nxs,:,nxs]*Gdata   #flip vectors according to spin flip * det(opM)
-    Mag = np.tile(Mag[:,nxs],len(SGMT)*Ncen).T.reshape((len(SGMT),-1))
-    if SGData['SGInv'] and not SGData['SGFixed']:
-        Mag = np.repeat(Mag,2,axis=0)                  #Mag same shape as Gdata
+    Mag = np.tile(Mag[:,nxs],Nops).T  #make Mag same length as Gdata
+    Gdata = Gdata/Mag       #normalze mag. moments
+    Gdata = np.inner(Gdata.T,uAmat).T*np.sqrt(nl.det(GS))
     Uij = np.array(G2lat.U6toUij(Uijdata))
     bij = Mast*Uij.T
@@ -1057 +1056 @@
     
 def StructureFactorDervMag(refDict,G,hfx,pfx,SGData,calcControls,parmDict):
-    '''Compute structure factor derivatives on blocks of reflections - for powders/nontwins only
+    '''Compute magnetic structure factor derivatives on blocks of reflections - for powders/nontwins only
     input:
     
@@ -1075 +1074 @@
     ast = np.sqrt(np.diag(G))
     GS = G/np.outer(ast,ast)
+    uAmat = G2lat.Gmat2AB(GS)[0]
     Mast = twopisq*np.multiply.outer(ast,ast)
     SGMT = np.array([ops[0].T for ops in SGData['SGOps']])
     SGT = np.array([ops[1] for ops in SGData['SGOps']])
     Ncen = len(SGData['SGCen'])
-    if SGData['SGFixed']:
-        Nops = len(SGMT)*Ncen
-    else:
-        Nops = len(SGMT)*Ncen*(1+SGData['SGInv'])
-    Amat,Bmat = G2lat.Gmat2AB(G)
+    Nops = len(SGMT)*Ncen
+    if not SGData['SGFixed']:
+        Nops *= (1+SGData['SGInv'])
+    Bmat = G2lat.Gmat2AB(G)[1]
     nRef = len(refDict['RefList'])
     Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \
@@ -1098 +1097 @@
     Gdata = SGData['MagMom'][nxs,:,nxs]*Gdata   #flip vectors according to spin flip
     Mag = np.tile(Mag[:,nxs],Nops).T  #make Mag same length as Gdata
+    Gdata = Gdata/Mag       #normalze mag. moments
+    Gdata = np.inner(Gdata.T,uAmat).T*np.sqrt(nl.det(GS))       #make unit vectors in Cartesian space
     dGdm = (1.-Gdata**2)                        #1/Mag removed - canceled out in dqmx=sum(dqdm*dGdm)
     dFdMx = np.zeros((nRef,mSize,3))
@@ -1111 +1112 @@
 #reflection processing begins here - big arrays!
     iBeg = 0
-    blkSize = 32       #no. of reflections in a block - optimized for speed
+    blkSize = 40       #no. of reflections in a block - optimized for speed
     while iBeg < nRef:
         iFin = min(iBeg+blkSize,nRef)
@@ -1131 +1132 @@
         MF = refDict['FF']['MF'][iBeg:iFin].T[Tindx].T   #Nref,Natm
         TMcorr = 0.539*(np.reshape(Tiso,Tuij.shape)*Tuij)[:,0,:]*Fdata*Mdata*MF/(2*Nops)     #Nref,Natm
-        if SGData['SGInv'] and not SGData['SGFixed']:
-            mphase = np.hstack((phase,-phase))
-            Uniq = np.hstack((Uniq,-Uniq))      #Nref,Nops,hkl
-            Hij = np.hstack((Hij,Hij))
+        if SGData['SGInv']:
+            if not SGData['SGFixed']:
+                mphase = np.hstack((phase,-phase))  #OK
+                Uniq = np.hstack((Uniq,-Uniq))      #Nref,Nops,hkl
+                Hij = np.hstack((Hij,Hij))
+            else:
+                mphase = phase
         else:
-            mphase = phase
+            mphase = phase                    #
         Hij = np.concatenate(np.array([Hij for cen in SGData['SGCen']]),axis=1)
         Uniq = np.hstack([Uniq for cen in SGData['SGCen']])
@@ -1153 +1157 @@
         dqmx2 = np.sum(dqmx,axis=1)   #matrix * vector = vector
 #        dqmx1 = np.swapaxes(np.swapaxes(np.inner(dqdm.T,dGdm.T),0,1),2,3)
-        dmx = NQ*Q*dGdM[:,nxs,:,:]-Q*dqmx2                                #*Mag canceled out of dqmx term
+        dmx = (NQ*Q*dGdM[:,nxs,:,:]-Q*dqmx2)/Mag                                #*Mag canceled out of dqmx term
         
         fam = Q*TMcorr[nxs,:,nxs,:]*cosm[nxs,:,:,:]*Mag[nxs,nxs,:,:]    #Mxyz,Nref,Nop,Natm

trunk/testDeriv.py

@@ -22 +22 @@
 
 import sys
-import cPickle
-import cProfile,pstats,StringIO
+import platform
+if '2' in platform.python_version_tuple()[0]:
+    import cPickle
+    import StringIO
+else:
+    import _pickle as cPickle
+    import io as StringIO
+import cProfile,pstats
 import wx
 import numpy as np
@@ -53 +59 @@
         self.testDerivMenu = wx.MenuBar()
         self.File = wx.Menu(title='')
-        self.File.Append(help='Open testDeriv.dat', id=wxID_FILEOPEN,
-             kind=wx.ITEM_NORMAL,text='Open testDeriv.dat file')
-        self.File.Append(help='Make derivative plots',id=wxID_MAKEPLOTS,
-            kind=wx.ITEM_NORMAL,text='Make plots')
-        self.File.Append(help='Exit from testDeriv', id=wxID_FILEEXIT, kind=wx.ITEM_NORMAL,
-            text='Exit')
+        self.File.Append(wxID_FILEOPEN,'Open testDeriv.dat file','Open testDeriv.dat')
+        self.File.Append(wxID_MAKEPLOTS,'Make plots','Make derivative plots')
+        self.File.Append(wxID_FILEEXIT,'Exit','Exit from testDeriv')
         self.Bind(wx.EVT_MENU, self.OnTestRead, id=wxID_FILEOPEN)
         self.Bind(wx.EVT_MENU,self.OnMakePlots,id=wxID_MAKEPLOTS)
@@ -93 +96 @@
                 testFile = dlg.GetPath()
                 file = open(testFile,'rb')
-                self.values = cPickle.load(file)
-                self.HistoPhases = cPickle.load(file)
-                (self.constrDict,self.fixedList,self.depVarList) = cPickle.load(file)
-                self.parmDict = cPickle.load(file)
-                self.varylist = cPickle.load(file)
-                self.calcControls = cPickle.load(file)
-                self.pawleyLookup = cPickle.load(file)
+                if '2' in platform.python_version_tuple()[0]:
+                    self.values = cPickle.load(file)
+                    self.HistoPhases = cPickle.load(file)
+                    (self.constrDict,self.fixedList,self.depVarList) = cPickle.load(file)
+                    self.parmDict = cPickle.load(file)
+                    self.varylist = cPickle.load(file)
+                    self.calcControls = cPickle.load(file)
+                    self.pawleyLookup = cPickle.load(file)
+                else:
+                    self.values = cPickle.load(file,encoding='Latin-1')
+                    self.HistoPhases = cPickle.load(file,encoding='Latin-1')
+                    (self.constrDict,self.fixedList,self.depVarList) = cPickle.load(file,encoding='Latin-1')
+                    self.parmDict = cPickle.load(file,encoding='Latin-1')
+                    self.varylist = cPickle.load(file,encoding='Latin-1')
+                    self.calcControls = cPickle.load(file,encoding='Latin-1')
+                    self.pawleyLookup = cPickle.load(file,encoding='Latin-1')
                 self.use = [False for i in range(len(self.varylist+self.depVarList))]
                 self.delt = [max(abs(self.parmDict[name])*0.0001,1e-6) for name in self.varylist+self.depVarList]