Changeset 3261

Timestamp:

Feb 5, 2018 11:44:57 AM (5 years ago)

Author:

vondreele

Message:

implement import of mcif with Crenel site fraction functions

Location:

trunk

Files:

• GSASIImath.py (modified) (1 diff)
• imports/G2phase_CIF.py (modified) (5 diffs)

trunk/GSASIImath.py

@@ -1681 +1681 @@
                     scof.append(spos[0][:3])
                     ccof.append(spos[0][3:])
-                if len(scof):
+                if len(scof):               #ToDo: something odd here, but it works
                     if icent < 0:                        
                         mom += np.sum(posFourier(.25-tauT,np.array(scof),np.array(ccof)),axis=1)

trunk/imports/G2phase_CIF.py

@@ -383 +383 @@
                 UijFloop = None
                 UijFdict = {}
+                #occupancy modulation
                 if blk.get('_atom_site_occ_Fourier_atom_site_label'):
                     occFloop = blk.GetLoop('_atom_site_occ_Fourier_atom_site_label')
@@ -389 +390 @@
                     occCloop = blk.GetLoop('_atom_site_occ_special_func_atom_site_label')
                     occCdict = dict(occCloop.items())
+                #position modulation
                 if blk.get('_atom_site_displace_Fourier_atom_site_label'):
                     displFloop = blk.GetLoop('_atom_site_displace_Fourier_atom_site_label')
@@ -395 +397 @@
                     displSloop = blk.GetLoop('_atom_site_displace_special_func_atom_site_label')
                     displSdict = dict(displSloop.items())
+                #U modulation
                 if blk.get('_atom_site_U_Fourier_atom_site_label'):
                     UijFloop = blk.GetLoop('_atom_site_U_Fourier_atom_site_label')
                     UijFdict = dict(UijFloop.items())
+                #Mag moment modulation
                 if blk.get('_atom_site_moment_Fourier_atom_site_label'):
                     MagFloop = blk.GetLoop('_atom_site_moment_Fourier_atom_site_label')
@@ -475 +479 @@
                     self.MPhase['Atoms'].append(matomlist)
                 if Super:
-                    Sfrac = []
+                    Sfrac = np.zeros((4,2))
                     Sadp = np.zeros((4,12))
                     Spos = np.zeros((4,6))
                     Smag = np.zeros((4,6))
                     nim = -1
-                    waveType = 'Fourier'                                
+                    waveType = 'Fourier'
+                    if  occCdict:
+                        for i,item in enumerate(occCdict['_atom_site_occ_special_func_atom_site_label']):
+                            if item == atomlist[0]:
+                                waveType = 'Crenel'
+                                val = occCdict['_atom_site_occ_special_func_crenel_c'][i]
+                                Sfrac[0][0] = cif.get_number_with_esd(val)[0]
+                                val = occCdict['_atom_site_occ_special_func_crenel_w'][i]
+                                Sfrac[0][1] = cif.get_number_with_esd(val)[0]
+                                nim = 1
+                    
+                    if nim >= 0:
+                        Sfrac = [[sfrac,False] for sfrac in Sfrac[:nim]]
+                    else:
+                        Sfrac = []
                     if displFdict:
                         for i,item in enumerate(displFdict['_atom_site_displace_fourier_atom_site_label']):
@@ -501 +519 @@
                         for i,item in enumerate(UijFdict['_atom_site_u_fourier_atom_site_label']):
                             if item == atomlist[0]:
+                                waveType = 'Fourier'                                
                                 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])