Changeset 2039

Timestamp:

Nov 2, 2015 3:36:00 PM (7 years ago)

Author:

vondreele

Message:

remove "crenelType" from SS atom data - won't be needed
implement Fourier modulations from cif files for position & Uijs (not Frac yet)

Location:

trunk

Files:

• GSASIIphsGUI.py (modified) (1 diff)
• imports/G2phase.py (modified) (4 diffs)
• imports/G2phase_CIF.py (modified) (3 diffs)

trunk/GSASIIphsGUI.py

@@ -1177 +1177 @@
 ################################################################################
 
-    SSdefault = {'SS1':{'waveType':'Fourier','crenelType':None,'Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}
+    SSdefault = {'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}
     def FillAtomsGrid(Atoms):
         '''Display the contents of the Atoms tab

trunk/imports/G2phase.py

@@ -465 +465 @@
             S1T = list(S1[60:63])
             waveType = waveTypes[int(S1T[1])]
-            crenelType = ''
             Spos = []
             Sadp = []
@@ -492 +491 @@
                     if int(S1T[0]):  #"", "Legendre" or "Xharm" in 18:27 for "crenel"!
                         waveType = 'Crenel/Fourier' #all waves 'Fourier' no other choice
-                        crenelType = FS[18:27]
                 Sfrac.append(file2.readline()[:18]) #if not crenel = Osin & Ocos
                 # else Osin & Ocos except last one is X40 = 'Center'
@@ -516 +514 @@
                 print Sfrac[i]
             for i,it in enumerate(Spos):
-                if waveType in ['ZigZag','Sawtooth'] and not i:
+                if waveType in ['Sawtooth',] and not i:
                     vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36])]
                 else:
@@ -533 +531 @@
             Atom.append([])
             Atom.append([])
-            Atom.append({'SS1':{'waveType':waveType,'crenelType':crenelType,'Sfrac':Sfrac,'Spos':Spos,'Sadp':Sadp,'Smag':Smag}})    #SS2 is for (3+2), etc.
+            Atom.append({'SS1':{'waveType':waveType,'Sfrac':Sfrac,'Spos':Spos,'Sadp':Sadp,'Smag':Smag}})    #SS2 is for (3+2), etc.
             Atoms.append(Atom)
         file2.close()

trunk/imports/G2phase_CIF.py

@@ -183 +183 @@
                     anisokeys = []
                     anisolabels = []
+                if Super:
+                    occFloop = None
+                    occCloop = None
+                    occFdict = {}
+                    cooCdict = {}
+                    displSloop = None
+                    displFloop = None
+                    dispSdict = {}
+                    dispFdict = {}
+                    UijFloop = None
+                    UijFdict = {}
+                    if blk.get('_atom_site_occ_Fourier_atom_site_label'):
+                        occFloop = blk.GetLoop('_atom_site_occ_Fourier_atom_site_label')
+                        occFdict = dict(occFloop.items())
+                    if blk.get('_atom_site_occ_special_func_atom_site_label'):  #Crenel (i.e. Block Wave) occ
+                        occCloop = blk.GetLoop('_atom_site_occ_special_func_atom_site_label')
+                        occCdict = dict(occCloop.items())
+                    if blk.get('_atom_site_displace_Fourier_atom_site_label'):
+                        displFloop = blk.GetLoop('_atom_site_displace_Fourier_atom_site_label')
+                        displFdict = dict(displFloop.items())                            
+                    if blk.get('_atom_site_displace_special_func_atom_site_label'): #sawtooth
+                        displSloop = blk.GetLoop('_atom_site_displace_special_func_atom_site_label')
+                        displSdict = dict(displSloop.items())
+                    if blk.get('_atom_site_U_Fourier_atom_site_label'):
+                        UijFloop = blk.GetLoop('_atom_site_U_Fourier_atom_site_label')
+                        UijFdict = dict(UijFloop.items())
                 self.Phase['Atoms'] = []
                 G2AtomDict = {  '_atom_site_type_symbol' : 1,
@@ -196 +222 @@
                                 '_atom_site_aniso_u_13' : 15,
                                 '_atom_site_aniso_u_23' : 16, }
-                G2SSAtomDict = {'_atom_site_occ_Fourier_wave_vector_seq_id' : 1,
-                                '_atom_site_occ_Fourier_param_cos' : 2,
-                                '_atom_site_occ_Fourier_param_sin' : 3,
-                                '_atom_site_displace_Fourier_axis' : 2,
-                                '_atom_site_displace_Fourier_wave_vector_seq_id' : 3,
-                                '_atom_site_displace_Fourier_param_cos' : 5,
-                                '_atom_site_displace_Fourier_param_sin' : 4,
-                                '_atom_site_U_Fourier_tens_elem' : 7,
-                                '_atom_site_U_Fourier_wave_vector_seq_id' : 8,
-                                '_atom_site_U_Fourier_param_cos' : 9,
-                                '_atom_site_U_Fourier_param_sin' : 10,  }
-
-                                    
 
                 ranIdlookup = {}
@@ -253 +266 @@
                     else:
                         atomlbllist.append(atomlist[0])
+                    if Super:
+                        Sfrac = []
+                        Sadp = []                      
+                        Spos = np.zeros((4,6))
+                        nim = -1
+                        for i,item in enumerate(displFdict['_atom_site_displace_Fourier_atom_site_label']):
+                            if item == atomlist[0]:
+                                waveType = 'Fourier'                                
+                                ix = ['x','y','z'].index(displFdict['_atom_site_displace_Fourier_axis'][i])
+                                im = int(displFdict['_atom_site_displace_Fourier_wave_vector_seq_id'][i])
+                                if im != nim:
+                                    nim = im
+                                val = displFdict['_atom_site_displace_Fourier_param_sin'][i]
+                                Spos[im-1][ix] = cif.get_number_with_esd(val)[0]
+                                val = displFdict['_atom_site_displace_Fourier_param_cos'][i]
+                                Spos[im-1][ix+3] = cif.get_number_with_esd(val)[0]
+                        if nim >= 0:
+                            Spos = [[spos,False] for spos in Spos[:nim]]
+                        else:
+                            Spos = []
+                        if UijFdict:
+                            nim = -1
+                            Sadp = np.zeros((4,12))
+                            for i,item in enumerate(UijFdict['_atom_site_U_Fourier_atom_site_label']):
+                                if item == atomlist[0]:
+                                    ix = ['U11','U22','U33','U12','U13','U23'].index(UijFdict['_atom_site_U_Fourier_tens_elem'][i])
+                                    im = int(UijFdict['_atom_site_U_Fourier_wave_vector_seq_id'][i])
+                                    if im != nim:
+                                        nim = im
+                                    val = UijFdict['_atom_site_U_Fourier_param_sin'][i]
+                                    Sadp[im-1][ix] = cif.get_number_with_esd(val)[0]
+                                    val = UijFdict['_atom_site_U_Fourier_param_cos'][i]
+                                    Sadp[im-1][ix+6] = cif.get_number_with_esd(val)[0]
+                            if nim >= 0:
+                                Sadp = [[sadp,False] for sadp in Sadp[:nim]]
+                            else:
+                                Sadp = []
+                        
+                        SSdict = {'SS1':{'waveType':waveType,'Sfrac':Sfrac,'Spos':Spos,'Sadp':Sadp,'Smag':[]}}
+                        atomlist.append(SSdict)
                 if len(atomlbllist) != len(self.Phase['Atoms']):
                     self.isodistort_warnings += '\nRepeated atom labels prevents ISODISTORT decode'