Changeset 2766

Timestamp:

Mar 30, 2017 1:31:01 PM (8 years ago)

Author:

vondreele

Message:

add display of optional vertical lines to PlotXY (used for reflectometry model boundaries)
fix getCellEsd - bad analytic math; now done empirically - now works

Location:

trunk

Files:

• GSASIIplot.py (modified) (3 diffs)
• GSASIIpwdGUI.py (modified) (7 diffs)
• GSASIIstrIO.py (modified) (2 diffs)

trunk/GSASIIplot.py ¶

@@ -2820 +2820 @@
             
 def PlotXY(G2frame,XY,XY2=None,labelX='X',labelY='Y',newPlot=False,
-    Title='',lines=False,names=[],names2=[]):
+    Title='',lines=False,names=[],names2=[],vertLines=[]):
     '''simple plot of xy data
     
@@ -2833 +2833 @@
     :param list of str names: legend names for each XY plot
     :param list of str names2: legend names for each XY2 plot
+    :param lists of vertical line x-positions list; can be one for each XY
     :return nothing
     
@@ -2906 +2907 @@
         else:
             Plot.plot(X,Y,colors[ixy%6]+'+',picker=False)
-    if XY2 and len(XY2):
+    if len(vertLines):
+        for ixy,X in enumerate(vertLines):
+            dX = Page.Offset[0]*(ixy+1)*Xmax/500.
+            for x in X:
+                Plot.axvline(x+dX,color=colors[ixy%6],dashes=(5,5),picker=False)
+    if XY2 is not None and len(XY2):
         for ixy,xy in enumerate(XY2):
             X,Y = XY2[ixy]

trunk/GSASIIpwdGUI.py ¶

@@ -4740 +4740 @@
         SaveState()
         G2pwd.REFDRefine(Profile,ProfDict,Inst,Limits,Substances,data)
-        x,xr,y = G2pwd.makeSLDprofile(data,Substances)
-        ModelPlot(data,x,xr,y)
+#        x,xr,y = G2pwd.makeSLDprofile(data,Substances)
+#        ModelPlot(data,x,xr,y)
         G2plt.PlotPatterns(G2frame,plotType='REFD')
         wx.CallLater(100,UpdateREFDModelsGrid,G2frame,data)
@@ -4782 +4782 @@
         
     def ModelPlot(data,x,xr,y):
+        nLines = len(data['Layers'])-1
+        linePos = np.zeros(nLines)
+        for ilay,layer in enumerate(data['Layers'][1:-1]):
+            linePos[ilay+1:] += layer['Thick'][0]
         if data['Zero']:
             XY = [[x,y],]
@@ -4788 +4792 @@
             XY = [[xr,y],]
             disLabel = r'$Distance\ from\ substrate,\ \AA$'
-        G2plt.PlotXY(G2frame,XY,labelX=disLabel,labelY=r'$SLD,\ 10^{10}cm^{-2}$',newPlot=False,
-            Title='Scattering length density',lines=True,names=[])
+        G2plt.PlotXY(G2frame,XY,labelX=disLabel,labelY=r'$SLD,\ 10^{10}cm^{-2}$',newPlot=True,
+            Title='Scattering length density',lines=True,names=[],vertLines=[linePos,])
         
     def OnUnDo(event):
@@ -4797 +4801 @@
         G2frame.dataFrame.REFDUndo.Enable(False)
         G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
-        x,xr,y = G2pwd.makeSLDprofile(data,Substances)
-        ModelPlot(data,x,xr,y)
+#        x,xr,y = G2pwd.makeSLDprofile(data,Substances)
+#        ModelPlot(data,x,xr,y)
         G2plt.PlotPatterns(G2frame,plotType='REFD')
         wx.CallLater(100,UpdateREFDModelsGrid,G2frame,data)
@@ -4822 +4826 @@
         def OnRefPos(event):
             data['Zero'] = refpos.GetValue()
+            x,xr,y = G2pwd.makeSLDprofile(data,Substances)
+            ModelPlot(data,x,xr,y)
             
         def OnMinSel(event):
@@ -4926 +4932 @@
                 return
             G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
-            x,xr,y = G2pwd.makeSLDprofile(data,Substances)
-            ModelPlot(data,x,xr,y)
+#            x,xr,y = G2pwd.makeSLDprofile(data,Substances)
+#            ModelPlot(data,x,xr,y)
             G2plt.PlotPatterns(G2frame,plotType='REFD')
             wx.CallLater(100,UpdateREFDModelsGrid,G2frame,data) 
@@ -5046 +5052 @@
     Size = mainSizer.Fit(G2frame.dataFrame)
     Size[0] += 25
-    G2frame.dataFrame.setSizePosLeft(Size)    
+    G2frame.dataFrame.setSizePosLeft(Size)
+    x,xr,y = G2pwd.makeSLDprofile(data,Substances)
+    ModelPlot(data,x,xr,y)
+    
     
 ################################################################################

trunk/GSASIIstrIO.py ¶

@@ -1534 +1534 @@
 def getCellEsd(pfx,SGData,A,covData):
     'needs a doc string'
-    dpr = 180./np.pi
     rVsq = G2lat.calc_rVsq(A)
     G,g = G2lat.A2Gmat(A)       #get recip. & real metric tensors
-    cell = np.array(G2lat.Gmat2cell(g))   #real cell
-    cellst = np.array(G2lat.Gmat2cell(G)) #recip. cell
-    scos = cosd(cellst[3:6])
-    ssin = sind(cellst[3:6])
-    scot = scos/ssin
-    rcos = cosd(cell[3:6])
-    rsin = sind(cell[3:6])
-    rcot = rcos/rsin
     RMnames = [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5']
     varyList = covData['varyList']
@@ -1559 +1550 @@
         vcov[1,2] = vcov[2,1] = vcov[0,2]
     elif SGData['SGLaue'] in ['3R','3mR']:
-        vcov[0:2,0:2] = vcov[0,0]
-        vcov[4,4] = vcov[5,5] = vcov[3,3]
+        vcov[0:3,0:3] = vcov[0,0]
+#        vcov[4,4] = vcov[5,5] = vcov[3,3]
+        vcov[3:6,3:6] = vcov[3,3]
         vcov[0:3,3:6] = vcov[0,3]
         vcov[3:6,0:3] = vcov[3,0]
-    Ax = np.array(A)
-    Ax[3:] /= 2.
-    drVdA = np.array([
-        Ax[1]*Ax[2]-Ax[5]**2,
-        Ax[0]*Ax[2]-Ax[4]**2,
-        Ax[0]*Ax[1]-Ax[3]**2,
-        Ax[4]*Ax[5]-Ax[2]*Ax[3],
-        Ax[3]*Ax[5]-Ax[1]*Ax[4],
-        Ax[3]*Ax[4]-Ax[0]*Ax[5]])
+    delt = 1.e-9
+    drVdA = np.zeros(6)
+    for i in range(6):
+        A[i] += delt
+        drVdA[i] = G2lat.calc_rVsq(A)
+        A[i] -= 2*delt
+        drVdA[i] -= G2lat.calc_rVsq(A)
+        A[i] += delt
+    drVdA /= 2.*delt    
     srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov))
     Vol = 1/np.sqrt(rVsq)
     sigVol = Vol**3*np.sqrt(srcvlsq)/2.         #ok - checks with GSAS
     
-    R123 = Ax[0]*Ax[1]*Ax[2]
-    dsasdg = np.zeros((3,6))
-    dadg = np.zeros((6,6))
-    for i0 in range(3):         #0  1   2
-        i1 = (i0+1)%3           #1  2   0
-        i2 = (i1+1)%3           #2  0   1
-        i3 = 5-i2               #3  5   4
-        i4 = 5-i1               #4  3   5
-        i5 = 5-i0               #5  4   3
-        dsasdg[i0][i1] = 0.5*scot[i0]*scos[i0]/Ax[i1]
-        dsasdg[i0][i2] = 0.5*scot[i0]*scos[i0]/Ax[i2]
-        dsasdg[i0][i5] = -scot[i0]/np.sqrt(Ax[i1]*Ax[i2])
-        denmsq = Ax[i0]*(R123-Ax[i1]*Ax[i4]**2-Ax[i2]*Ax[i3]**2)+(Ax[i4]*Ax[i3])**2
-        denom = np.sqrt(denmsq)
-        dadg[i5][i0] = -Ax[i5]/denom-rcos[i0]/denmsq*(R123-0.5*Ax[i1]*Ax[i4]**2-0.5*Ax[i2]*Ax[i3]**2)
-        dadg[i5][i1] = -0.5*rcos[i0]/denmsq*(Ax[i0]**2*Ax[i2]-Ax[i0]*Ax[i4]**2)
-        dadg[i5][i2] = -0.5*rcos[i0]/denmsq*(Ax[i0]**2*Ax[i1]-Ax[i0]*Ax[i3]**2)
-        dadg[i5][i3] = Ax[i4]/denom+rcos[i0]/denmsq*(Ax[i0]*Ax[i2]*Ax[i3]-Ax[i3]*Ax[i4]**2)
-        dadg[i5][i4] = Ax[i3]/denom+rcos[i0]/denmsq*(Ax[i0]*Ax[i1]*Ax[i4]-Ax[i3]**2*Ax[i4])
-        dadg[i5][i5] = -Ax[i0]/denom
-    for i0 in range(3):
-        i1 = (i0+1)%3
-        i2 = (i1+1)%3
-        i3 = 5-i2
-        for ij in range(6):
-            dadg[i0][ij] = cell[i0]*(rcot[i2]*dadg[i3][ij]/rsin[i2]-dsasdg[i1][ij]/ssin[i1])
-            if ij == i0:
-                dadg[i0][ij] = dadg[i0][ij]-0.5*cell[i0]/Ax[i0]
-            dadg[i3][ij] = -dadg[i3][ij]*rsin[2-i0]*dpr
-#    GSASIIpath.IPyBreak()
-    sigMat = np.inner(dadg,np.inner(dadg,vcov))
+    dcdA = np.zeros((6,6))
+    for i in range(6):
+        pdcdA =np.zeros(6)
+        A[i] += delt
+        pdcdA += G2lat.A2cell(A)
+        A[i] -= 2*delt
+        pdcdA -= G2lat.A2cell(A)
+        A[i] += delt
+        dcdA[i] = pdcdA/(2.*delt)
+    
+    sigMat = np.inner(dcdA,np.inner(dcdA,vcov))
     var = np.diag(sigMat)
     CS = np.where(var>0.,np.sqrt(var),0.)