Changeset 3295

Timestamp:

Feb 22, 2018 11:01:07 AM (5 years ago)

Author:

vondreele

Message:

remove superfluous calls to SpcGroup? after SGData has been defined
add 3rd row magnetic form factors
add contour plots for projections of mustrain, size, % 3D pole distribution
improve quality of these surfaces

Location:

trunk

Files:

• GSASIIElem.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (10 diffs)
• GSASIIplot.py (modified) (3 diffs)
• GSASIIspc.py (modified) (6 diffs)
• atmdata.py (modified) (1 diff)

trunk/GSASIIElem.py

@@ -380 +380 @@
     nt = -nfb[:,np.newaxis]*SQ
     MMF = np.sum(mfa[:,np.newaxis]*np.exp(mt)[:],axis=0)+El['mfc']
+    MMF0 = np.sum(mfa)+El['mfc']
     NMF = np.sum(nfa[:,np.newaxis]*np.exp(nt)[:],axis=0)+El['nfc']
-    return MMF+(2.0/El['gfac']-1.0)*NMF
+    NMF0 = np.sum(nfa)+El['nfc']
+    MF0 = MMF0+(2.0/El['gfac']-1.0)*NMF0
+    return (MMF+(2.0/El['gfac']-1.0)*NMF)/MF0
         
 def BlenResCW(Els,BLtables,wave):

trunk/GSASIIphsGUI.py

@@ -2499 +2499 @@
                 ci = colLabels.index('I/A')
                 ID = atomData[r][ci+8]
+                SGData = generalData['SGData']
                 if Atoms.GetColLabelValue(c) in ['x','y','z']:
                     ci = colLabels.index('x')
@@ -2506 +2507 @@
                     SScol = colLabels.index('site sym')
                     Mulcol = colLabels.index('mult')
-                    E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
                     Sytsym,Mult = G2spc.SytSym(XYZ,SGData)[:2]
                     atomData[r][SScol] = Sytsym
@@ -2556 +2556 @@
                     ci = colLabels.index('I/A')
                     atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][ci+8],''),'')
+                elif Atoms.GetColLabelValue(c) in ['Mx','My','Mz']:
+                    value = atomData[r][c]
+                    cx = colLabels.index('x')
+                    SpnFlp = generalData['SGData']['SpnFlp']
+                    SytSym,Mul,Nop,dupDir = G2spc.SytSym(atomData[r][cx:cx+3],SGData)
+                    CSI = G2spc.GetCSpqinel(SytSym,SpnFlp,dupDir)
+                    iM = CSI[0][c-colLabels.index('Mx')]
+                    for i in range(3):
+                        if iM == CSI[0][i]:
+                            atomData[r][i+colLabels.index('Mx')] = value*CSI[1][i]
                 if 'Atoms' in data['Drawing']:
                     ci = colLabels.index('I/A')
@@ -2720 +2730 @@
                     if not SGData['SGGray']:
                         CSI = G2spc.GetCSpqinel(SytSym,SpnFlp,dupDir)
-#                    print (SytSym,Nop,SpnFlp[Nop],CSI,dupDir)
+                    print (SytSym,Nop,SpnFlp[Nop],CSI,dupDir)
                     for i in range(3):
                         ci = i+colM
@@ -2728 +2738 @@
                             Atoms.SetCellStyle(row,ci,WHITE,False)
                             Atoms.SetCellTextColour(row,ci,BLACK)
-                            
                 if 'X' in rbExcl:
                     for c in range(0,colX+3):
@@ -2837 +2846 @@
         generalData = data['General']
         atId = ran.randint(0,sys.maxsize)
-        E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
+        SGData = generalData['SGData']
         Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)[:2]
         if generalData['Type'] == 'macromolecular':
@@ -3086 +3095 @@
         atomData = data['Atoms']
         generalData = data['General']
-        E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
+        SGData = generalData['SGData']
         Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)[:2]
         atId = ran.randint(0,sys.maxsize)
@@ -3178 +3187 @@
         atomData = data['Atoms']
         generalData = data['General']
+        ifMag = False
         colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
         ci = colLabels.index('I/A')
@@ -3183 +3193 @@
         if generalData['Type'] == 'magnetic':
             choices += ['Mx','My','Mz',]
+            ifMag = True
         dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
         parm = ''
@@ -3191 +3202 @@
         dlg.Destroy()
         if parm in ['Type']:
-            dlg = G2elemGUI.PickElement(G2frame)
+            dlg = G2elemGUI.PickElement(G2frame,ifMag=ifMag)
             if dlg.ShowModal() == wx.ID_OK:
                 if dlg.Elem not in ['None']:

trunk/GSASIIplot.py

@@ -3964 +3964 @@
     G2frame.G2plotNB.status.SetStatusText('',1)
     
-    PHI = np.linspace(0.,360.,30,True)
-    PSI = np.linspace(0.,180.,30,True)
+    PHI = np.linspace(0.,360.,40,True)
+    PSI = np.linspace(0.,180.,40,True)
     X = np.outer(npcosd(PHI),npsind(PSI))
     Y = np.outer(npsind(PHI),npsind(PSI))
@@ -4039 +4039 @@
             xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
             XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
+            Plot.contour(X,Y,Z,10,zdir='x',offset=XYZlim[0])
+            Plot.contour(X,Y,Z,10,zdir='y',offset=XYZlim[1])
+            Plot.contour(X,Y,Z,10,zdir='z',offset=XYZlim[0])
             Plot.set_xlim3d(XYZlim)
             Plot.set_ylim3d(XYZlim)
@@ -4305 +4308 @@
                 xyzlim = np.array([Plot.get_xlim3d(),Plot.get_ylim3d(),Plot.get_zlim3d()]).T
                 XYZlim = [min(xyzlim[0]),max(xyzlim[1])]
+                Plot.contour(X,Y,Z,10,zdir='x',offset=XYZlim[0])
+                Plot.contour(X,Y,Z,10,zdir='y',offset=XYZlim[1])
+                Plot.contour(X,Y,Z,10,zdir='z',offset=XYZlim[0])
                 Plot.set_xlim3d(XYZlim)
                 Plot.set_ylim3d(XYZlim)

trunk/GSASIIspc.py

@@ -178 +178 @@
                 moregen.append(1)
     SGData['SGGen'] += moregen
-#    GSASIIpath.IPyBreak()
     if SGData['SGLaue'] in '-1':
         SGData['SGSys'] = SysSym[0]
@@ -542 +541 @@
     LaueSym = ('-1','2/m','mmm','4/m','4/mmm','3R','3mR','3','3m1','31m','6/m','6/mmm','m3','m3m')
     LattSym = ('P','A','B','C','I','F','R')
-    UniqSym = ('','','a','b','c','',)
     
     '''
@@ -1720 +1718 @@
     Idup = []
     Cell = []
+    inv = int(SGData['SGInv']+1)
+    icen = SGData['SGCen']
+    if SGData['SGFixed']:
+        inv = 1
     X = np.array(XYZ)
     if Move:
         X = MoveToUnitCell(X)[0]
-    for ic,cen in enumerate(SGData['SGCen']):
+    for ic,cen in enumerate(icen):
         C = np.array(cen)
-        for invers in range(int(SGData['SGInv']+1)):
+        for invers in range(inv):
             for io,[M,T] in enumerate(SGData['SGOps']):
                 idup = ((io+1)+100*ic)*(1-2*invers)
@@ -2092 +2094 @@
     "returns Mxyz terms, multipliers, GUI flags"
     CSI = [[1,2,3],[1.0,1.0,1.0]]
+    if '-1' in siteSym and SpnFlp[len(SpnFlp)//2] < 0:
+        return [[0,0,0],[0.,0.,0.]]
     for opr in dupDir:
-        if '-1' in siteSym and SpnFlp[len(SpnFlp)//2] < 0:
-            return [[0,0,0],[0.,0.,0.]]
         indx = GetNXUPQsym(opr)
         if SpnFlp[dupDir[opr]] > 0.:
@@ -2100 +2102 @@
         else:
             csi = CSxinel[indx[3]]  #Q
+        print(opr,SpnFlp[dupDir[opr]],indx,csi,CSI)
         if not len(csi):
             return [[0,0,0],[0.,0.,0.]]
@@ -2847 +2850 @@
     Ndup = 0
     dupDir = {}
+    inv = SGData['SGInv']+1
+    icen = SGData['SGCen']
+    if SGData['SGFixed']:       #already in list of operators
+        inv = 1
     Xeqv = GenAtom(XYZ,SGData,True)
     IRT = PackRot(SGData['SGOps'])
     L = -1
-    for ic,cen in enumerate(SGData['SGCen']):
-        for invers in range(int(SGData['SGInv']+1)):
+    for ic,cen in enumerate(icen):
+        for invers in range(int(inv)):
             for io,ops in enumerate(SGData['SGOps']):
                 irtx = (1-2*invers)*IRT[io]

trunk/atmdata.py

@@ -24 +24 @@
            <j0> & <j2> coeff. from Intl. Tables for Cryst, Vol. C
            5-d <j0> & <j2> from Kobayashi K, Nagao T, Ito M.
-           Acta Crystallogr A68, 589-94 (2012)
+           Acta Crystallogr A67, 473-480 (2011)
 
            Neutron anomalous coeff (LS) from fitting Lynn & Seeger, At. Data & Nuc. Data Tables, 44, 191-207(1990)