Changeset 4865 for trunk

Timestamp:

Mar 24, 2021 1:06:49 PM (2 years ago)

Author:

vondreele

Message:

fixes to monoclinic A,C,I centered cell indexing (still need to do P)
fix bug in bond restraints & add enhancement to atom requests for bonds, angles & planes.
Remove 'U' from open in G2phase.py - deprecated

Location:

trunk

Files:

• GSASIIindex.py (modified) (4 diffs)
• GSASIIrestrGUI.py (modified) (5 diffs)
• imports/G2phase.py (modified) (3 diffs)

trunk/GSASIIindex.py

@@ -873 +873 @@
             Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
             Asave.append([calc_M20(peaks,HKL,ifX20),Aref[:]])
-            if ibrav in [9,10,11]:                          #C-centered orthorhombic
+            if ibrav in [9,10,11]:                          #A,B,or C-centered orthorhombic
                 for i in range(2):
                     Abeg = rotOrthoA(Abeg[:])
@@ -900 +900 @@
     'needs a doc string'
     a,b,c,alp,bet,gam = G2lat.A2cell(A)
+    print(a,b,c,alp,bet,gam)
+    if bet < 90.: 
+        bet = 180.-bet     #always want obtuse beta
+        A = G2lat.cell2A([a,b,c,90.,bet,90.])
     G,g = G2lat.A2Gmat(A)
-    if ibrav in [13,]:    #I-monoclinic
-        pass
-        # u = [-1,0,0]
-        # v = [1,0,1]
-        # cnew = math.sqrt(np.dot(np.dot(v,g),v))
-        # if cnew < c:
-        #     cang = np.dot(np.dot(u,g),v)/(a*cnew)
-        #     beta = acosd(-abs(cang))
-        #     if beta < 90.: beta = 180.-beta
-        #     A = G2lat.cell2A([a,b,cnew,90,beta,90])
+    if ibrav in [13,]:    #I-monoclinic - checked OK
+        u = [-1,0,0]
+        v = [2,0,1]
+        cnew = math.sqrt(np.dot(np.dot(v,g),v))
+        if cnew < c:
+            cang = np.dot(np.dot(u,g),v)/(a*cnew)
+            beta = acosd(-abs(cang))
+            if beta < 90.: beta = 180.-beta     #always want obtuse beta
+            A = G2lat.cell2A([a,b,cnew,90,beta,90])
     elif ibrav in [14,]:      #A-monoclinic - OK?
         u = [0,0,-1]
@@ -918 +921 @@
             cang = np.dot(np.dot(u,g),v)/(anew*c)
             beta = acosd(-abs(cang))
-            if beta < 90.: beta = 180.-beta
+            if beta < 90.: beta = 180.-beta     #always want obtuse beta
             A = G2lat.cell2A([anew,b,c,90,beta,90])
     elif ibrav in [15,]:    #C-monoclinic - OK?
@@ -927 +930 @@
             cang = np.dot(np.dot(u,g),v)/(a*cnew)
             beta = acosd(-abs(cang))
-            if beta < 90.: beta = 180.-beta
+            if beta < 90.: beta = 180.-beta     #always want obtuse beta
             A = G2lat.cell2A([a,b,cnew,90,beta,90])
     return A

trunk/GSASIIrestrGUI.py

@@ -242 +242 @@
         Lists = {'origin':[],'target':[]}
         for listName in ['origin','target']:
-            dlg = wx.MultiChoiceDialog(G2frame,'Bond restraint '+listName+' for '+General['Name'],
+            dlg = G2G.G2MultiChoiceDialog(G2frame,'Bond restraint '+listName+' for '+General['Name'],
                     'Select bond restraint '+listName+' atoms',Names)
             if dlg.ShowModal() == wx.ID_OK:
@@ -276 +276 @@
                 for Tid,Ttype,Tcoord in targAtoms:
                     if 'macro' in General['Type']:
-                        result = [Tcoord,1,[0,0,0],[]]
+                        result = [[Tcoord,1,[0,0,0],[]],]
                     else:
                         result = G2spc.GenAtom(Tcoord,SGData,False,Move=False)
@@ -369 +369 @@
         Lists = {'A-atom':[],'B-atom':[],'C-atom':[]}
         for listName in ['A-atom','B-atom']:
-            dlg = wx.MultiChoiceDialog(G2frame,'Select '+listName+' for angle A-B-C for '+General['Name']                                                                           ,
+            dlg = G2G.G2MultiChoiceDialog(G2frame,'Select '+listName+' for angle A-B-C for '+General['Name']                                                                           ,
                     'Select angle restraint '+listName,Names)
             if dlg.ShowModal() == wx.ID_OK:
@@ -521 +521 @@
     def AddPlaneRestraint(restrData):
         ids = []
-        dlg = wx.MultiChoiceDialog(G2frame,'Select 4 or more atoms for plane in '+General['Name'],
+        dlg = G2G.G2MultiChoiceDialog(G2frame,'Select 4 or more atoms for plane in '+General['Name'],
                 'Select 4+ atoms',Names[iBeg:])
         if dlg.ShowModal() == wx.ID_OK:
@@ -812 +812 @@
         ids = []
         factors = []
-        dlg = wx.MultiChoiceDialog(G2frame,'Select atoms for chemical restraint in '+General['Name'],
+        dlg = G2G.G2MultiChoiceDialog(G2frame,'Select atoms for chemical restraint in '+General['Name'],
                 'Select atoms',Names)
         if dlg.ShowModal() == wx.ID_OK:

trunk/imports/G2phase.py

@@ -76 +76 @@
         EightPiSq = 8.*math.pi**2
         self.errors = 'Error opening file'
-        file = open(filename, 'Ur')
+        file = open(filename, 'r')
         Phase = {}
         Title = os.path.basename(filename)
@@ -449 +449 @@
         '''
         self.errors = 'Error opening file'
-        fp = open(filename, 'Ur') #contains only cell & spcgroup
+        fp = open(filename, 'r') #contains only cell & spcgroup
         Phase = {}
         Title = os.path.basename(filename)
@@ -523 +523 @@
         waveTypes = ['Fourier','Sawtooth','ZigZag',]
         filename2 = os.path.splitext(filename)[0]+'.m40'
-        file2 = open(filename2,'Ur')
+        file2 = open(filename2,'r')
         S = file2.readline()
         line = 1