Changeset 3163

Timestamp:

Nov 28, 2017 10:06:41 AM (5 years ago)

Author:

vondreele

Message:

fix typo in Tb neutron scattering factors; extra space
fix lst output of neutron resonant form factors - computations were correct
implement import of mcif files.

Location:

trunk

Files:

• GSASIIstrIO.py (modified) (1 diff)
• atmdata.py (modified) (1 diff)
• imports/G2phase_CIF.py (modified) (7 diffs)

trunk/GSASIIstrIO.py

@@ -860 +860 @@
             isotope = bldata[0]
             mass = bldata[1]['Mass']
-            if 'SL' in bldata[1]:
+            if 'BW-LS' in bldata[1]:
+                bres = bldata[1]['BW-LS']
+                blen = 0
+            else:
                 blen = bldata[1]['SL'][0]
                 bres = []
-            else:
-                blen = 0
-                bres = bldata[1]['BW-LS']
             line = ' %8s%11s %10.3f %8.3f'%(Ename.ljust(8),isotope.center(11),mass,blen)
             for item in bres:

trunk/atmdata.py

@@ -525 +525 @@
         'BW-LS':[  0.683,      88.78, 4684.9, 28.11, 52.61,0,0,0,0]},     #LS
     'Gd_160':{'Mass':159.927,'SL':[   .915,      0],'SA':         .77},
-    'Tb_ ':  {'Mass':158.925,'SL':[   .734,      0],'SA':        23.4},
+    'Tb_':  {'Mass':158.925,'SL':[   .734,      0],'SA':        23.4},
     'Tb_159':{'Mass':158.925,'SL':[   .734,      0],'SA':        23.4},
     'Dy_':   {'Mass': 162.50,'SL':[   1.69,      0],'SA':        994.},

trunk/imports/G2phase_CIF.py

@@ -38 +38 @@
     def __init__(self):
         super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__
-            extensionlist=('.CIF','.cif','.txt'),
+            extensionlist=('.CIF','.cif','.txt','.mcif'),
             strictExtension=False,
             formatName = 'CIF',
@@ -128 +128 @@
             E = True
             Super = False
+            magnetic = False
+            self.Phase['General']['Type'] = 'nuclear'
             SpGrp = blk.get("_symmetry_space_group_name_H-M",'')
             if not SpGrp:
                 SpGrp = blk.get("_space_group_name_H-M_alt",'')
+            if not SpGrp:
+                SpGrp = blk.get("_parent_space_group.name_H-M",'')
+                magnetic = True
+                self.Phase['General']['Type'] = 'magnetic'
+                self.Phase['General']['AtomPtrs'] = [3,1,10,12]
             if not SpGrp:
                 sspgrp = blk.get("_space_group_ssg_name",'').split('(')
@@ -170 +177 @@
             if not blk.get('_atom_site_type_symbol'):
                 self.isodistort_warnings += '\natom types are missing. \n Check & revise atom types as needed'
+            if magnetic:
+                magatomloop = blk.GetLoop('_atom_site_moment_label')
+                magatomkeys = [i.lower() for i in magatomloop.keys()]
             if blk.get('_atom_site_aniso_label'):
                 anisoloop = blk.GetLoop('_atom_site_aniso_label')
@@ -217 +227 @@
                             '_atom_site_aniso_u_13' : 15,
                             '_atom_site_aniso_u_23' : 16, }
+            G2MagDict = {'_atom_site_moment_label': 0,
+                         '_atom_site_moment_crystalaxis_x':7,
+                         '_atom_site_moment_crystalaxis_y':8,
+                         '_atom_site_moment_crystalaxis_z':9}
 
             ranIdlookup = {}
             for aitem in atomloop:
-                atomlist = ['','','',0,0,0,1.0,'',0,'I',0.01,0,0,0,0,0,0,0]
+                if magnetic:
+                    atomlist = ['','','',0.,0.,0.,1.0,0.,0.,0.,'',0.,'I',0.01,0.,0.,0.,0.,0.,0.,0.]
+                else:
+                    atomlist = ['','','',0.,0.,0.,1.0,'',0.,'I',0.01,0.,0.,0.,0.,0.,0.,0.]
                 atomlist[-1] = ran.randint(0,sys.maxsize) # add a random Id
                 while atomlist[-1] in ranIdlookup:
@@ -234 +251 @@
                                '_atom_site_adp_type'):   #Iso or Aniso?
                         if val.lower() == 'uani':
-                            atomlist[9] = 'A'
+                            if magnetic:
+                                atomlist[12] = 'A'
+                            else:
+                                atomlist[9] = 'A'
                     elif key == '_atom_site_u_iso_or_equiv':
                         uisoval = cif.get_number_with_esd(val)[0]
-                        if uisoval is not None: atomlist[10] = uisoval
+                        if uisoval is not None: 
+                            if magnetic:
+                                atomlist[13] = uisoval                                
+                            else:    
+                                atomlist[10] = uisoval
                 if not atomlist[1] and atomlist[0]:
                     typ = atomlist[0].rstrip('0123456789-+')
@@ -246 +270 @@
                         self.warnings += ' Atom type '+typ+' not recognized; Xe assumed\n'
                 if atomlist[0] in anisolabels: # does this atom have aniso values in separate loop?
-                    atomlist[9] = 'A'  # set the aniso flag
+                    if magnetic:
+                        atomlist[12] = 'A'
+                    else:
+                        atomlist[9] = 'A'
                     for val,key in zip( # load the values
                             anisoloop.GetKeyedPacket('_atom_site_aniso_label',atomlist[0]), 
                             anisokeys):
                         col = G2AtomDict.get(key)
+                        if magnetic:
+                            col += 3
                         if col:
                             atomlist[col] = cif.get_number_with_esd(val)[0]
-                atomlist[7],atomlist[8] = G2spc.SytSym(atomlist[3:6],SGData)[:2]
+                if magnetic:
+                    for mitem in magatomloop:
+                        matom = mitem[G2MagDict.get('_atom_site_moment_label',-1)]
+                        if atomlist[0] == matom:
+                            for mval,mkey in zip(mitem,magatomkeys):
+                                mcol = G2MagDict.get(mkey,-1)
+                                if mcol:
+                                    atomlist[mcol] = cif.get_number_with_esd(mval)[0]
+                            break                            
+                    atomlist[10],atomlist[11] = G2spc.SytSym(atomlist[3:6],SGData)[:2]
+                else:
+                    atomlist[7],atomlist[8] = G2spc.SytSym(atomlist[3:6],SGData)[:2]
                 atomlist[1] = G2elem.FixValence(atomlist[1])
                 self.Phase['Atoms'].append(atomlist)
@@ -316 +356 @@
             self.Phase['General']['Name'] = name.strip()[:20]
             self.Phase['General']['Super'] = Super
+            if magnetic:
+                self.Phase['General']['Type'] = 'magnetic'                
             if Super:
                 self.Phase['General']['Type'] = 'modulated'