Changeset 2808

Timestamp:

Apr 25, 2017 2:01:51 PM (8 years ago)

Author:

vondreele

Message:

small fixes to reflectometry calcs.
fix Hessian restraint bug - wrong sign for Vec
add theta, refl, (sig) import option for reflectometry

Location:

trunk

Files:

• GSASIIpwd.py (modified) (2 diffs)
• GSASIIpwdGUI.py (modified) (4 diffs)
• GSASIIstrMath.py (modified) (1 diff)
• imports/G2rfd_xye.py (modified) (4 diffs)

trunk/GSASIIpwd.py ¶

@@ -1986 +1986 @@
             line = ' '
             line2 = ' Scattering density: Real %.5g'%(Substances[name]['Scatt density']*parmDict[cid+'DenMul'])
-            line2 += ' Imag %.5g'%(Substances[name].get('XImag density',0.)**parmDict[cid+'DenMul'])
+            line2 += ' Imag %.5g'%(Substances[name].get('XImag density',0.)*parmDict[cid+'DenMul'])
             for parm in ['Thick','Rough','DenMul','Mag SLD','iDenMul']:
                 if parm in layer:
@@ -2170 +2170 @@
             sigma[ilay] = max(0.001,layer['Rough'][0])
         if name != 'vacuum':
-            rho[ilay] = Substances[name]['Scatt density']*layer['DenMul'][0]
+            if name == 'unit scatter':
+                rho[ilay] = np.sqrt(layer['DenMul'][0]**2+layer['iDenMul'][0]**2)
+            else:
+                rrho = Substances[name]['Scatt density']
+                irho = Substances[name]['XImag density']
+                rho[ilay] = np.sqrt(rrho**2+irho**2)*layer['DenMul'][0]
         if 'Mag SLD' in layer:
             rho[ilay] += layer['Mag SLD'][0]

trunk/GSASIIpwdGUI.py ¶

@@ -227 +227 @@
     return {'Layers':[{'Name':'vacuum','DenMul':[1.0,False],},                                  #top layer
         {'Name':'vacuum','Rough':[0.,False],'Penetration':[0.,False],'DenMul':[1.0,False],}],   #bottom layer
-        'Scale':[1.0,False],'FltBack':[0.0,False],'Zero':'Top','dQ type':'None',                #globals
+        'Scale':[1.0,False],'FltBack':[0.0,False],'Zero':'Top','dQ type':'None','Layer Seq':[],               #globals
         'Minimizer':'LMLS','Resolution':[0.,'Const dq/q'],'Recomb':0.5,'Toler':0.5,             #minimizer controls
         'DualFitFiles':['',],'DualFltBacks':[[0.0,False],],'DualScales':[[1.0,False],]}         #optional stuff for multidat fits?
@@ -4972 +4972 @@
         def OndQSel(event):
             data['dQ type'] = dQSel.GetStringSelection()
+            Recalculate()
+            
+        def NewRes(invalid,value,tc):
+            Recalculate()
+            
+        def Recalculate():
+            G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
+            x,xr,y = G2pwd.makeSLDprofile(data,Substances)
+            ModelPlot(data,x,xr,y)
+            G2plt.PlotPatterns(G2frame,plotType='REFD')
             
         controlSizer = wx.BoxSizer(wx.VERTICAL)
@@ -4984 +4994 @@
         resol.Add(dQSel,0,WACV)
         resol.Add(wx.StaticText(G2frame.dataDisplay,label=' (FWHM %): '),0,WACV)
-        resol.Add(G2G.ValidatedTxtCtrl(G2frame.dataDisplay,data['Resolution'],0,nDig=(10,3),min=0.,max=5.),0,WACV)
+        resol.Add(G2G.ValidatedTxtCtrl(G2frame.dataDisplay,data['Resolution'],0,nDig=(10,3),min=0.,max=5.,OnLeave=NewRes),0,WACV)
         controlSizer.Add(resol,0,WACV)
         minimiz = wx.BoxSizer(wx.HORIZONTAL)
@@ -5102 +5112 @@
             ModelPlot(data,x,xr,y)
             G2plt.PlotPatterns(G2frame,plotType='REFD')
-            wx.CallLater(100,UpdateREFDModelsGrid,G2frame,data) 
+#            wx.CallLater(100,UpdateREFDModelsGrid,G2frame,data) 
 
         Indx = {}                       

trunk/GSASIIstrMath.py ¶

@@ -3733 +3733 @@
     if np.any(pVals):
         dpdv = penaltyDeriv(pNames,pVals,HistoPhases,calcControls,parmDict,varylist)
-        Vec += np.sum(dpdv*pWt*pVals,axis=1)
+        Vec -= np.sum(dpdv*pWt*pVals,axis=1)
         Hess += np.inner(dpdv*pWt,dpdv)
     return Vec,Hess

trunk/imports/G2rfd_xye.py ¶

@@ -22 +22 @@
 GSASIIpath.SetVersionNumber("$Revision: 2738 $")
 npasind = lambda x: 180.*np.arcsin(x)/np.pi
+npsind = lambda x: np.sin(np.pi*x/180.)
+fourpi = 4.0*np.pi
 
 class txt_XRayReaderClass(G2IO.ImportReflectometryData):
@@ -92 +94 @@
                         y.append(float(data[1]))
                         w.append(1.0/(0.02*float(data[1]))**2)
+                        sq.append(0.)
                 except ValueError:
                     msg = 'Error in line '+str(i+1)
@@ -191 +194 @@
                         y.append(float(data[1]))
                         w.append(1.0/(0.02*float(data[1]))**2)
+                        sq.append(0.)
                 except ValueError:
                     msg = 'Error in line '+str(i+1)
@@ -221 +225 @@
         return True
 
+class txt_XRayThetaReaderClass(G2IO.ImportReflectometryData):
+    'Routines to import X-ray theta REFD data from a .xtrfd or .xtdat file'
+    def __init__(self):
+        super(self.__class__,self).__init__( # fancy way to self-reference
+            extensionlist=('.xtrfd','.xtdat'),
+            strictExtension=False,
+            formatName = 'theta step X-ray QRE data',
+            longFormatName = 'theta stepped X-ray text data file in Q,R,E order; E optional'
+            )
+
+    # Validate the contents -- make sure we only have valid lines
+    def ContentsValidator(self, filepointer):
+        'Look through the file for expected types of lines in a valid q-step file'
+        Ndata = 0
+        self.wavelength = 0.
+        for i,S in enumerate(filepointer):
+            if '#' in S[0]:
+                if 'wavelength' in S[:-1].lower():
+                    self.wavelength = float(S[:-1].split('=')[1])
+                elif 'energy' in S[:-1].lower():
+                    self.wavelength = 12.39842*1000./float(S[:-1].split('=')[1])
+                continue
+            vals = S.split()
+            if len(vals) >= 2:
+                try:
+                    data = [float(val) for val in vals]
+                    Ndata += 1
+                except ValueError:
+                    pass
+        if not Ndata:     
+            self.errors = 'No 2 or more column numeric data found'
+            return False
+        elif not self.wavelength:
+            self.errors = 'Missing wavelength or energy in header'
+            return False
+        return True # no errors encountered
+
+    def Reader(self,filename,filepointer, ParentFrame=None, **unused):
+        print 'Read a q-step text file'
+        x = []
+        y = []
+        w = []
+        sq = []
+        wave = self.wavelength
+        Temperature = 300
+        for i,S in enumerate(filepointer):
+            if len(S) == 1:     #skip blank line
+                continue
+            if '=' in S:
+                self.comments.append(S[:-1])
+                if 'wave' in S.split('=')[0].lower():
+                    try:
+                        wave = float(S.split('=')[1])
+                    except:
+                        pass
+                continue
+            if '#' in S[0]:
+                continue
+            vals = S.split()
+            if len(vals) >= 2:
+                try:
+                    data = [float(val) for val in vals]
+                    x.append(fourpi*npsind(float(data[0]))/wave)
+                    f = float(data[1])
+                    if f <= 0.0:
+                        del x[-1]
+                        continue
+                    elif len(vals) > 2:
+                        y.append(float(data[1]))
+                        w.append(1.0/float(data[2])**2)
+                        if len(vals) == 4:
+                            sq.append(float(data[3]))
+                        else:
+                            sq.append(0.)
+                    else:
+                        y.append(float(data[1]))
+                        w.append(1.0/(0.02*float(data[1]))**2)
+                        sq.append(0.)
+                except ValueError:
+                    msg = 'Error in line '+str(i+1)
+                    print msg
+                    continue
+        N = len(x)
+        for S in self.comments:
+            if 'Temp' in S.split('=')[0]:
+                try:
+                    Temperature = float(S.split('=')[1])
+                except:
+                    pass
+        self.instdict['wave'] = wave
+        self.instdict['type'] = 'RXC'
+        x = np.array(x)
+        self.reflectometrydata = [
+            x, # x-axis values q
+            np.array(y), # small angle pattern intensities
+            np.array(w), # 1/sig(intensity)^2 values (weights)
+            np.zeros(N), # calc. intensities (zero)
+            np.zeros(N), # obs-calc profiles
+            np.array(sq), # fix bkg
+            ]
+        self.reflectometryentry[0] = filename
+        self.reflectometryentry[2] = 1 # xye file only has one bank
+        self.idstring = ospath.basename(filename)
+        # scan comments for temperature
+        self.Sample['Temperature'] = Temperature
+
+        return True
+