Changeset 4450

Timestamp:

May 31, 2020 12:06:22 PM (4 years ago)

Author:

vondreele

Message:

Add Histogram bonds & angles to Atoms/Compute? menu - makes histogram plots of bonds & angles about selected atoms

Location:

trunk

Files:

• GSASIIdataGUI.py (modified) (2 diffs)
• GSASIIphsGUI.py (modified) (5 diffs)
• GSASIIplot.py (modified) (1 diff)
• GSASIIstrMain.py (modified) (1 diff)

trunk/GSASIIdataGUI.py

@@ -5989 +5989 @@
             'wxID_RELOADDRAWATOMS', 'wxID_ATOMSDISAGL', 'wxID_ATOMMOVE', 'wxID_MAKEMOLECULE',
             'wxID_ATOMSPDISAGL', 'wxID_ISODISP', 'wxID_ADDHATOM', 'wxID_UPDATEHATOM',
-            'wxID_ATOMSROTATE', 'wxID_ATOMSDENSITY', 
+            'wxID_ATOMSROTATE', 'wxID_ATOMSDENSITY','wxID_ATOMSBNDANGLHIST', 
             'wxID_ATOMSSETALL', 'wxID_ATOMSSETSEL',)
         self.AtomsMenu = wx.MenuBar()
@@ -6026 +6026 @@
         self.AtomCompute.Append(G2G.wxID_ATOMSDISAGL,'Show Distances && Angles','Compute distances & angles for selected atoms')
         self.AtomCompute.Append(G2G.wxID_ATOMSPDISAGL,'Save Distances && Angles','Compute distances & angles for selected atoms')
+        self.AtomCompute.Append(G2G.wxID_ATOMSBNDANGLHIST,'Histogram Bonds && Angles','Histogram bonds & angles for selected atoms')
         self.AtomCompute.Append(G2G.wxID_ATOMSDENSITY,'Density','Compute density for current phase')
         self.AtomCompute.ISOcalc = self.AtomCompute.Append(G2G.wxID_ISODISP,'ISODISTORT mode values',

trunk/GSASIIphsGUI.py

@@ -4102 +4102 @@
         fp.close()
     
-    def OnDistAngle(event,fp=None):
+    def OnDistAngleHist(event):
+        OnDistAngle(event,hist=True)
+        
+    def OnDistAngle(event,fp=None,hist=False):
         'Compute distances and angles'    
         indx = getAtomSelections(Atoms)
@@ -4126 +4129 @@
             cx = colLabels.index('x')
             cn = colLabels.index('Name')
+            ct = colLabels.index('Type')
+            Atypes = []
             for i,atom in enumerate(atomData):
                 xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
                 if i in indx:
                     Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
+                    Atypes.append(atom[ct])
+            Atypes = set(Atypes)
+            Atypes = ', '.join(Atypes)
             DisAglData['OrigAtoms'] = Oxyz
             DisAglData['TargAtoms'] = xyz
@@ -4139 +4147 @@
                 DisAglData['covData'] = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Covariance'))
             try:
-                if fp:
+                if hist:
+                    AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(DisAglCtls,DisAglData)
+                    Bonds = []
+                    for dists in DistArray:
+                        Bonds += [item[3] for item in DistArray[dists]]
+                    G2plt.PlotBarGraph(G2frame,Bonds,Xname=r'$\mathsf{Bonds,\AA}$',
+                        Title='Bond distances for %s'%Atypes,PlotName='%s Bonds'%Atypes)
+                    Angles = []
+                    for angles in AngArray:
+                        Angles += [item[2][0] for item in AngArray[angles]]
+                    G2plt.PlotBarGraph(G2frame,Angles,Xname='$\mathsf{Angles,{^o}}$',
+                        Title='Bond angles about %s'%Atypes,PlotName='%s Angles'%Atypes)
+                    
+                elif fp:
                     G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
                 else:    
@@ -5691 +5712 @@
                                         impangles = 180.*item.get_constraint_value()['angles']/np.pi
                                         impangleList = item.anglesList[:4]
+                                        print(' Dihedral angle chi^2 =  %2f'%item.standardError)
                                         atoms = ENGINE.get_original_data("allElements",frame)
                                         impangleNames = ['%s-%s-%s-%s'%(atoms[impangleList[0][iat]],atoms[impangleList[1][iat]],
@@ -11796 +11818 @@
         G2frame.Bind(wx.EVT_MENU, OnDistAngle, id=G2G.wxID_ATOMSDISAGL)
         G2frame.Bind(wx.EVT_MENU, OnDistAnglePrt, id=G2G.wxID_ATOMSPDISAGL)
+        G2frame.Bind(wx.EVT_MENU, OnDistAngleHist, id=G2G.wxID_ATOMSBNDANGLHIST)
         G2frame.Bind(wx.EVT_MENU, OnDensity, id=G2G.wxID_ATOMSDENSITY)
         G2frame.Bind(wx.EVT_MENU, OnIsoDistortCalc, id=G2G.wxID_ISODISP)

trunk/GSASIIplot.py

@@ -5297 +5297 @@
         wid = Dbins[1]-Dbins[0]
     else:
-        nBins= max(10,len(Xarray)//10)
+        nBins= min(40,max(10,len(Xarray)//10))
         if maxBins is not None:
             nBins = min(nBins,maxBins)

trunk/GSASIIstrMain.py

@@ -666 +666 @@
                                 unit = Units[indb][i]
                                 tunit = (unit[0]+Tunit[0],unit[1]+Tunit[1],unit[2]+Tunit[2])
-                                pdpx = G2mth.getDistDerv(Oatom[3:6],Tatom[3:6],Amat,unit,Top,SGData)
                                 sig = 0.0
                                 if len(Xvcov):
+                                    pdpx = G2mth.getDistDerv(Oatom[3:6],Tatom[3:6],Amat,unit,Top,SGData)
                                     sig = np.sqrt(np.inner(pdpx,np.inner(pdpx,Xvcov)))
                                 Dist.append([Oatom[0],Tatom[0],tunit,Top,ma.getdata(dist[indb])[i],sig])