Changeset 4265 for trunk

Timestamp:

Jan 25, 2020 12:47:07 PM (5 years ago)

Author:

vondreele

Message:

add bond direction plots to RMCProfile results

Location:

trunk

Files:

• GSASIIphsGUI.py (modified) (6 diffs)
• GSASIIplot.py (modified) (1 diff)
• GSASIIpwd.py (modified) (1 diff)

trunk/GSASIIphsGUI.py ¶

@@ -4468 +4468 @@
                     'atSeq':atSeq,'Pairs':Pairs,'histogram':['',1.0],'files':files,'metadata':metadata,
                     'runTimes':runTimes,'ReStart':[False,False],'BVS':BVS,'Oxid':atOxid,'useBVS':False,'Swaps':[],
-                    'AveCN':[],'FxCN':[],'Potentials':{'Angles':[],'Angle search':10.,'Stretch':[],'Stretch search':10.,
+                    'AveCN':[],'FxCN':[],'Potentials':{'Angles':[],'Angle search':10.,'Stretch':[],
+                    'Stretch search':10.,'Pot. Temp.':300.,
                     }}
             RMCPdict = data['RMC']['RMCProfile']
@@ -4492 +4493 @@
                 RMCPdict.update({'AveCN':[],'FxCN':[]})
             if 'Potentials' not in RMCPdict:
-                RMCPdict.update({'Potentials':{'Angles':[],'Angle search':10.,'Stretch':[],'Stretch search':10.}})
+                RMCPdict.update({'Potentials':{'Angles':[],'Angle search':10.,'Stretch':[],'Stretch search':10.,'Pot. Temp.':300.,}})
+            if 'Pot. Temp.' not in RMCPdict['Potentials']:
+                RMCPdict['Potentials']['Pot. Temp.'] = 300.
             if 'Swaps' not in RMCPdict:
                 RMCPdict['Swaps'] = []
@@ -4913 +4916 @@
                 
             G2G.HorizontalLine(mainSizer,G2frame.FRMC)
+            pottempBox = wx.BoxSizer(wx.HORIZONTAL)
+            pottempBox.Add(wx.StaticText(G2frame.FRMC,label=' Potential temperature (K): '),0,WACV)
+            pottempBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Potentials'],'Pot. Temp.',min=0.,max=1000.,size=(50,25)),0,WACV)
+            mainSizer.Add(pottempBox,0,WACV)
+            bondpotBox = wx.BoxSizer(wx.HORIZONTAL)
+            bondpotAdd = wx.Button(G2frame.FRMC,label='Add')
+            bondpotAdd.Bind(wx.EVT_BUTTON,OnAddBondPot)
+            bondpotBox.Add(bondpotAdd,0,WACV)
+            bondpotBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B stretch potential restraints, search range (%): '),0,WACV)
+            bondpotBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Potentials'],'Stretch search',min=0.,max=100.,size=(50,25)),0,WACV)
+            mainSizer.Add(bondpotBox,0,WACV)
+            if len(RMCPdict['Potentials']['Stretch']):
+                mainSizer.Add(GetBondSizer(),0,WACV)
+
             angpotBox = wx.BoxSizer(wx.HORIZONTAL)
             angpotAdd = wx.Button(G2frame.FRMC,label='Add')
@@ -4923 +4940 @@
                 mainSizer.Add(GetAngleSizer(),0,WACV)
                 
-            G2G.HorizontalLine(mainSizer,G2frame.FRMC)
-            bondpotBox = wx.BoxSizer(wx.HORIZONTAL)
-            bondpotAdd = wx.Button(G2frame.FRMC,label='Add')
-            bondpotAdd.Bind(wx.EVT_BUTTON,OnAddBondPot)
-            bondpotBox.Add(bondpotAdd,0,WACV)
-            bondpotBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B stretch potential restraints, search range (%): '),0,WACV)
-            bondpotBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Potentials'],'Stretch search',min=0.,max=100.,size=(50,25)),0,WACV)
-            mainSizer.Add(bondpotBox,0,WACV)
-            if len(RMCPdict['Potentials']['Stretch']):
-                mainSizer.Add(GetBondSizer(),0,WACV)
-
             G2G.HorizontalLine(mainSizer,G2frame.FRMC)
             mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' Select data:'),0,WACV)
@@ -5171 +5177 @@
             generalData = data['General']
             RMCPdict = data['RMC']['RMCProfile']
+            atSeq = RMCPdict['atSeq']
             pName = generalData['Name'].replace(' ','_')
             dlg = wx.FileDialog(G2frame, "Choose any RMCProfile csv results file for "+pName+":",
@@ -5275 +5282 @@
                     labelY=r'$\mathsf{\chi^2}$',newPlot=True,Title='RMCP Chi^2 for '+pName,
                     lines=True,names=Names[3:])
-        
+#bond odf plots                
+            nPot = len(RMCPdict['Potentials']['Stretch'])
+            for iPot in range(nPot):
+                fname = pName+'.bondodf_%d'%(iPot+1)
+                bond = RMCPdict['Potentials']['Stretch'][iPot]
+                if os.path.exists(os.path.join(path,fname)):
+                    OutFile = open(fname,'r')
+                    odfFile = OutFile.readlines()
+                    if len(odfFile) > 1:
+                        OutFile.seek(0)
+                        odfData = np.fromfile(OutFile,sep=' ')
+                        numx,numy = odfData[:2]
+                        G2plt.Plot3dXYZ(G2frame,int(numx),int(numy),odfData[2:],newPlot=False,Title='Bond %s-%s'%(bond[0],bond[1]))        
         
             

trunk/GSASIIplot.py ¶

@@ -5109 +5109 @@
         
 ################################################################################
+##### Plot3dXYZ
+################################################################################
+        
+def Plot3dXYZ(G2frame,nX,nY,Zdat,labelX='X',labelY='Y',labelZ='Z',newPlot=False,Title=''):
+    
+    def OnMotion(event):
+        xpos = event.xdata
+        if xpos:                                        #avoid out of frame mouse position
+            ypos = event.ydata
+            G2frame.G2plotNB.status.SetStatusText('X =%.3f Y =%.4f'%(xpos,ypos),1)                   
+            
+    def OnKeyPress(event):
+        if event.key == 'g':
+            mpl.rcParams['axes.grid'] = not mpl.rcParams['axes.grid']
+
+    new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab(Title,'3d')
+    if not new:
+        if not Page.IsShown():
+            Page.Show()
+    else:
+        Page.canvas.mpl_connect('motion_notify_event', OnMotion)
+    Page.Choice = None
+    G2frame.G2plotNB.status.SetStatusText('',1)
+    Zmul = Zdat.reshape((nX,-1)).T
+    PHI = np.linspace(0.,360.,int(nY),True)
+    PSI = np.linspace(0.,180.,int(nX),True)
+    X = Zmul*np.outer(npcosd(PHI),npsind(PSI))/2.
+    Y = Zmul*np.outer(npsind(PHI),npsind(PSI))/2.
+    Z = Zmul*np.outer(np.ones(np.size(PHI)),npcosd(PSI))/2.
+    
+    if np.any(X) and np.any(Y) and np.any(Z):
+        np.seterr(all='ignore')
+        Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
+        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)
+        Plot.set_zlim3d(XYZlim)
+        try:
+            Plot.set_aspect('equal')
+        except: #broken in mpl 3.1.1; worked in mpl 3.0.3
+            pass
+        Plot.set_title(Title)
+        Plot.set_xlabel(labelX)
+        Plot.set_ylabel(labelY)
+        Plot.set_zlabel(labelZ)
+    Page.canvas.draw()
+        
+################################################################################
 ##### PlotHist
 ################################################################################

trunk/GSASIIpwd.py ¶

@@ -2358 +2358 @@
         fl.write('\n')
         fl.write('POTENTIALS ::\n')
+        fl.write('  > TEMPERATURE :: %.1f K\n'%RMCPdict['Potentials']['Pot. Temp.'])
+        fl.write('  > PLOT :: pixels=400, colour=red, zangle=90, zrotation=45 deg\n')
         if len(RMCPdict['Potentials']['Stretch']):
             fl.write('  > STRETCH_SEARCH :: %.1f%%\n'%RMCPdict['Potentials']['Stretch search'])