Changeset 612

Timestamp:

May 11, 2012 10:35:51 AM (11 years ago)

Author:

vondreele

Message:

complete combined x/n exercise & fix bugs uncovered in process
made version 0.2.0
moved tutorials in help menu to be 2nd
fixed problem with drawing after f-map generated
fixed some plot errors
reverse sign on macrostrain

Location:

trunk

Files:

• Exercises/PbSO4/INST_XRY.PRM (modified) (1 diff)
• Exercises/PbSO4/PbSO4.gpx (deleted)
• Exercises/kryptonite/kryptonite.gpx (deleted)
• Exercises/two phase/AB-Si3N4.gpx (modified) (previous)
• GSASII.py (modified) (1 diff)
• GSASIIgrid.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (4 diffs)
• GSASIIplot.py (modified) (4 diffs)
• GSASIIstruct.py (modified) (4 diffs)

trunk/Exercises/PbSO4/INST_XRY.PRM

@@ -1 @@
-            123456789012345678901234567890123456789012345678901234567890        
+            123456789012345678901234567890123456789012345678901234567890
 INS   BANK      1                                                               
 INS   HTYPE   PXCR                                                              
 INS  1 IRAD     3                                                               
 INS  1 ICONS  1.540500  1.544300       0.0         0       0.7    0       0.5   
-INS  1I HEAD  DUMMY INCIDENT SPECTRUM FOR X-RAY DIFFRACTOMETER                  
+INS  1I HEAD  DUMMY INCIDENT SPECTRUM FOR X-RAY DIFFRACTOMETER
 INS  1I ITYP    0    0.0000  180.0000         1                                 
 INS  1PRCF1     3    8      0.01                                                
 INS  1PRCF11   2.000000E+00  -2.000000E+00   5.000000E+00   0.100000E+00        
 INS  1PRCF12   0.000000E+00   0.000000E+00   0.150000E-01   0.150000E-01        
-INS  1PRCF2     2    6      0.01                                                
-INS  1PRCF21   2.000000E+00  -2.000000E+00   5.000000E+00   0.100000E+01        
-INS  1PRCF22   0.100000E+01   0.000000E+00                                      
-INS  1PRCF3     4   12      0.01                                                
-INS  1PRCF31   2.000000E+00  -2.000000E+00   5.000000E+00   0.000000E+00        
-INS  1PRCF32   0.100000E+00   0.000000E+00   0.000000E+00   0.000000E+00        
-INS  1PRCF33   0.000000E+00   0.150000E-01   0.150000E-01   0.750000E+00        

trunk/GSASII.py

@@ -84 +84 @@
     pass
 #    print "MKL module not present"
-__version__ = '0.1.5'
+__version__ = '0.2.0'
 G2gd.__version__ = __version__
 print "This is GSAS-II version:     ",__version__

trunk/GSASIIgrid.py

@@ -143 +143 @@
             frame.Bind(wx.EVT_MENU, self.OnHelpById, helpobj)
             self.HelpById[helpobj.GetId()] = helpType
-        self.Append(help='', id=wx.ID_ABOUT, kind=wx.ITEM_NORMAL,
-            text='&About GSAS-II')
-        frame.Bind(wx.EVT_MENU, self.OnHelpAbout, id=wx.ID_ABOUT)
         for lbl,indx in morehelpitems:
             helpobj = self.Append(text=lbl,
@@ -151 +148 @@
             frame.Bind(wx.EVT_MENU, self.OnHelpById, helpobj)
             self.HelpById[helpobj.GetId()] = indx
+        self.Append(help='', id=wx.ID_ABOUT, kind=wx.ITEM_NORMAL,
+            text='&About GSAS-II')
+        frame.Bind(wx.EVT_MENU, self.OnHelpAbout, id=wx.ID_ABOUT)
 
     def OnHelpById(self,event):

trunk/GSASIIphsGUI.py

@@ -1442 +1442 @@
 #        elif generalData['Type'] == 'modulated':
 #           ?????   for future
-        if not drawingData['Atoms']:
+        if not drawingData.get('Atoms'):
             for atom in atomData:
                 DrawAtomAdd(drawingData,atom)
@@ -1782 +1782 @@
             dlg.Destroy()
             G2frame.dataFrame.SetStatusText('')
+            G2plt.PlotStructure(G2frame,data)
             
     def ResetAtomColors(event):
@@ -3644 +3645 @@
         mapData['Flip'] = False
         mapSig = np.std(mapData['rho'])
+        if not data['Drawing']:                 #if new drawing - no drawing data!
+            SetupDrawingData()
         data['Drawing']['contourLevel'] = 1.
         data['Drawing']['mapSize'] = 10.
         print mapData['MapType']+' computed: rhomax = %.3f rhomin = %.3f sigma = %.3f'%(np.max(mapData['rho']),np.min(mapData['rho']),mapSig)
+        UpdateDrawAtoms()
         G2plt.PlotStructure(G2frame,data)
         
@@ -3701 +3705 @@
         G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksMove, id=G2gd.wxID_PEAKSMOVE)
         G2frame.dataFrame.Bind(wx.EVT_MENU, OnPeaksClear, id=G2gd.wxID_PEAKSCLEAR)
+        UpdateDrawAtoms()
         FillMapPeaksGrid()
         G2plt.PlotStructure(G2frame,data)

trunk/GSASIIplot.py

@@ -425 +425 @@
                     wave = Parms['Lam1']
                 if G2frame.qPlot:
-                    xpos = 2.0*asind(xpos*wave/(4*math.pi))
+                    try:
+                        xpos = 2.0*asind(xpos*wave/(4*math.pi))
+                    except ValueError:      #avoid bad value in asin beyond upper limit
+                        pass
                 dsp = 0.0
                 if abs(xpos) > 0.:                  #avoid possible singularity at beam center
@@ -550 +553 @@
             Phases = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId,'Reflection Lists'))
             pick = str(G2frame.itemPicked).split('(')[1].strip(')')
-            if 'Line' not in pick:       #avoid data points, etc.
+            if 'line' not in pick:       #avoid data points, etc.
                 num = Phases.keys().index(pick)
                 if num:
@@ -750 +753 @@
             for pId,phase in enumerate(Phases):
                 peaks = Phases[phase]
+                if not peaks:
+                    continue
                 peak = np.array([[peak[4],peak[5]] for peak in peaks])
                 pos = G2frame.refOffset-pId*Ymax*G2frame.refDelt*np.ones_like(peak)
@@ -758 +763 @@
             if len(Phases):
                 handles,legends = Plot.get_legend_handles_labels()  #got double entries in the legends for some reason
-                Plot.legend(handles[::2],legends[::2],title='Phases',loc='best')    #skip every other one
+                if handles:
+                    Plot.legend(handles[::2],legends[::2],title='Phases',loc='best')    #skip every other one
             
     if G2frame.Contour:

trunk/GSASIIstruct.py

@@ -2306 +2306 @@
         Dij = parmDict[phfx+'D11']*h**2+parmDict[phfx+'D22']*k**2+parmDict[phfx+'D33']*l**2+ \
             parmDict[phfx+'D12']*h*k+parmDict[phfx+'D13']*h*l+parmDict[phfx+'D23']*k*l
-    return Dij*refl[4]**2*tand(refl[5]/2.0)
+    return -Dij*refl[4]**2*tand(refl[5]/2.0)
             
 def GetHStrainShiftDerv(refl,SGData,phfx):
@@ -2336 +2336 @@
             phfx+'D12':h*k,phfx+'D13':h*l,phfx+'D23':k*l}
     for item in dDijDict:
-        dDijDict[item] *= refl[4]**2*tand(refl[5]/2.0)
+        dDijDict[item] *= -refl[4]**2*tand(refl[5]/2.0)
     return dDijDict
     
@@ -2394 +2394 @@
                         Wd,fmin,fmax = G2pwd.getWidths(refl[5],refl[6],refl[7],shl)
                         iBeg = max(xB,np.searchsorted(x,refl[5]-fmin))
-                        iFin = min(np.searchsorted(x,refl[5]+fmax),xF)
+                        iFin = max(xB,min(np.searchsorted(x,refl[5]+fmax),xF))
                         iFin2 = iFin
                         yp[iBeg:iFin] = refl[13]*refl[9]*G2pwd.getFCJVoigt3(refl[5],refl[6],refl[7],shl,x[iBeg:iFin])    #>90% of time spent here
@@ -2400 +2400 @@
                             pos2 = refl[5]+lamRatio*tand(refl[5]/2.0)       # + 360/pi * Dlam/lam * tan(th)
                             Wd,fmin,fmax = G2pwd.getWidths(pos2,refl[6],refl[7],shl)
-                            iBeg2 = max(xB,np.searchsorted(x[xB:xF],pos2-fmin))
-                            iFin2 = min(np.searchsorted(x[xB:xF],pos2+fmax),xF)
+                            iBeg2 = max(xB,np.searchsorted(x,pos2-fmin))
+                            iFin2 = min(np.searchsorted(x,pos2+fmax),xF)
+                            if not iBeg2+iFin2:       #peak below low limit - skip peak
+                                continue
+                            elif not iBeg2-iFin2:     #peak above high limit - done
+                                break
                             yp[iBeg2:iFin2] += refl[13]*refl[9]*kRatio*G2pwd.getFCJVoigt3(pos2,refl[6],refl[7],shl,x[iBeg2:iFin2])        #and here
                         refl[8] = np.sum(np.where(ratio[iBeg:iFin2]>0.,yp[iBeg:iFin2]*ratio[iBeg:iFin2]/(refl[13]*(1.+kRatio)),0.0))