Changeset 1935

Timestamp:

Jul 20, 2015 9:25:46 AM (7 years ago)

Author:

vondreele

Message:

apply Uiso (equiv) for H-atom generation/update
revise H-atom addition to allow consecutive addition
deleted H atoms treated correctly

Location:

trunk

Files:

• GSASIImath.py (modified) (8 diffs)
• GSASIIphsGUI.py (modified) (5 diffs)

trunk/GSASIImath.py

@@ -421 +421 @@
     Oatom = GetAtomsById(Atoms,AtLookUp,[AddHydId[0],])[0]
     OXYZ = np.array(Oatom[cx:cx+3])
+    if 'I' in Oatom[cia]:
+        Uiso = Oatom[cia+1]
+    else:
+        Uiso = (Oatom[cia+2]+Oatom[cia+3]+Oatom[cia+4])/3.0       #simple average
+    Uiso = max(Uiso,0.005)                      #set floor!
     Tatoms = GetAtomsById(Atoms,AtLookUp,AddHydId[1])
     TXYZ = np.array([tatom[cx:cx+3] for tatom in Tatoms]) #3 x xyz
@@ -431 +436 @@
             Len = np.sqrt(np.sum(Vec**2))
             Hpos = OXYZ-0.98*np.inner(Bmat,Vec).T/Len
-            return [Hpos,]
+            HU = 1.1*Uiso
+            return [Hpos,],[HU,]
         elif AddHydId[-1] == 2:
             Vec = np.inner(Amat,TXYZ-OXYZ).T
@@ -442 +448 @@
             Hpos = np.array([[-0.97*cosd(54.75),0.97*sind(54.75),0.],
                 [-0.97*cosd(54.75),-0.97*sind(54.75),0.]])
+            HU = 1.2*Uiso*np.ones(2)
             Hpos = np.inner(Bmat,np.inner(iMat,Hpos).T).T+OXYZ
-            return Hpos
+            return Hpos,HU
         else:
             Ratom = GetAtomsById(Atoms,AtLookUp,[AddHydId[2],])[0]
@@ -452 +459 @@
             Hpos = np.array([[a,0.,-b],[a,-b*cosd(30.),0.5*b],[a,b*cosd(30.),0.5*b]])
             Hpos = np.inner(Bmat,np.inner(iMat,Hpos).T).T+OXYZ
-            return Hpos            
+            HU = 1.5*Uiso*np.ones(3)
+            return Hpos,HU          
     elif nBonds == 3:
         if AddHydId[-1] == 1:
@@ -459 +467 @@
             Vec = -0.93*Vec/Len
             Hpos = OXYZ+Vec
-            return [Hpos,]
+            HU = 1.1*Uiso
+            return [Hpos,],[HU,]
         elif AddHydId[-1] == 2:
             Ratom = GetAtomsById(Atoms,AtLookUp,[AddHydId[2],])[0]
@@ -468 +477 @@
             Hpos = [[a,b,0],[a,-b,0]]
             Hpos = np.inner(Bmat,np.inner(iMat,Hpos).T).T+OXYZ
-            return Hpos
+            HU = 1.2*Uiso*np.ones(2)
+            return Hpos,HU
     else:   #2 bonds
         if 'C' in Oatom[ct]:
@@ -475 +485 @@
             Vec = -0.93*Vec/Len
             Hpos = OXYZ+Vec
-            return [Hpos,]
+            HU = 1.1*Uiso
+            return [Hpos,],[HU,]
         elif 'O' in Oatom[ct]:
             mapData = General['Map']
@@ -488 +499 @@
             Rhos = np.array([getRho(pos,mapData) for pos in Hpos])
             imax = np.argmax(Rhos)
-            return [Hpos[imax],]
-    return []
+            HU = 1.5*Uiso
+            return [Hpos[imax],],[HU,]
+    return [],[]
         
 def AtomUij2TLS(atomData,atPtrs,Amat,Bmat,rbObj):   #unfinished & not used

trunk/GSASIIphsGUI.py

@@ -157 +157 @@
                 generalData['4DmapData'] = mapDefault.copy()
                 generalData['4DmapData'].update({'MapType':'Fobs'})
+        if 'HydIds' not in generalData:
+            generalData['HydIds'] = {}
 # end of patches
         cx,ct,cs,cia = generalData['AtomPtrs']
@@ -1188 +1190 @@
                             else:                           #'A' --> 'I'
                                 Uij = atomData[r][ui:ui+6]
-                                Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
+                                Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0   
                                 atomData[r][us] = Uiso
                                 Atoms.SetCellStyle(r,us,WHITE,False)
@@ -1600 +1602 @@
                             mapError = True
                             continue                            
-                        Hxyz = G2mth.AddHydrogens(AtLookUp,generalData,atomData,AddHydIds[ineigh])
+                        Hxyz,HU = G2mth.AddHydrogens(AtLookUp,generalData,atomData,AddHydIds[ineigh])
                         for iX,X in enumerate(Hxyz):
                             Nat += 1
                             AtomAdd(X[0],X[1],X[2],'H','H(%d)'%(Nat))
+                            data['Atoms'][-1][cia+1] = HU[iX]
                             Id = data['Atoms'][-1][cia+8]
                             HydIds[Id] = [iX,AddHydIds[ineigh]]
@@ -1609 +1612 @@
                     G2frame.ErrorDialog('Add H atom error','Adding O-H atoms requires delt-F map')
                 SetupGeneral()
-                data['General']['HydIds'] = HydIds
+                data['General']['HydIds'].update(HydIds)
                 G2frame.dataFrame.AtomEdit.Enable(G2gd.wxID_UPDATEHATOM,True)
                 FillAtomsGrid(Atoms)
@@ -1624 +1627 @@
         AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8)
         HydIds = data['General']['HydIds']
+        delList = []
         for HId in HydIds:
             hydIds = HydIds[HId]
             num = hydIds[0]
-            Hxyz = G2mth.AddHydrogens(AtLookUp,generalData,atomData,hydIds[1])
+            Hxyz,HU = G2mth.AddHydrogens(AtLookUp,generalData,atomData,hydIds[1])
             try:
                 data['Atoms'][AtLookUp[HId]][cx:cx+3] = Hxyz[num]
+                data['Atoms'][-1][cia+1] = HU[num]
             except KeyError:
-                Error += 'Hydrogen atom not in atom list - ignored\n'
+                delList.append(HId)
                 continue
+        for HId in delList: #clear out deleted H-atoms
+            del HydIds[HId]
         data['Drawing']['Atoms'] = []
         UpdateDrawAtoms()
         FillAtomsGrid(Atoms)
         G2plt.PlotStructure(G2frame,data)
-        if Error:
-            wx.MessageBox(Error,caption=' H atom update Error',style=wx.ICON_EXCLAMATION)
         
     def OnAtomMove(event):