Changeset 1606


Ignore:
Timestamp:
Dec 13, 2014 10:51:53 AM (7 years ago)
Author:
vondreele
Message:

more FillAtomLookUp? errors
a few more orthorhombic SS symbols
some fixes for missing/deleted phases

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASII.py

    r1605 r1606  
    27492749                            if len(refList):
    27502750                                for i,item in DelList:
    2751                                     del(refList[item])
     2751                                    if item in refList:
     2752                                        del(refList[item])
    27522753                            self.PatternTree.SetItemPyData(Id,refList)
    27532754                        item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
  • trunk/GSASIIobj.py

    r1604 r1606  
    12941294        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
    12951295        'constr([0-9]*)' : 'Parameter from constraint',
    1296         # supersymmetry parameters
     1296        # supersymmetry parameters  'Flen','Fcent'?
    12971297        'mV([0-2])' : 'Modulation vector component \\1',
    1298 #        'Flen','Fcent','Fsin','Fcos'
     1298        'Fsin'  :   'Sin site fraction modulation',
     1299        'Fcos'  :   'Cos site fraction modulation',
    12991300        '[XYZ]sin'  : 'Sin position wave for \\1',
    13001301        '[XYZ]cos'  : 'Cos position wave for \\1',
  • trunk/GSASIIphsGUI.py

    r1605 r1606  
    39723972        if refresh:
    39733973            RigidBodies.DestroyChildren()
    3974         AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
    39753974        general = data['General']
    3976         cx = general['AtomPtrs'][0]
     3975        cx,ct,cs,cia = generalData['AtomPtrs']
     3976        AtLookUp = G2mth.FillAtomLookUp(data['Atoms'],cia+8)
    39773977        Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
    39783978        RBData = G2frame.PatternTree.GetItemPyData(   
     
    43444344        RBIds = dict(zip(RBNames,rbKeys))
    43454345        general = data['General']
     4346        cx,ct,cs,cia = generalData['AtomPtrs']
    43464347        Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
    43474348        Atoms = data['Atoms']
    4348         AtLookUp = G2mth.FillAtomLookUp(Atoms)
     4349        AtLookUp = G2mth.FillAtomLookUp(Atoms,cia+8)
    43494350        if 'macro' not in general['Type']:
    43504351            print '**** ERROR - this phase is not a macromolecule ****'
     
    44294430       
    44304431    def OnGlobalResRBTherm(event):
    4431         AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
    44324432        RBObjs = data['RBModels']['Residue']
    44334433        names = ['None','Uiso','T','TL','TLS']
    44344434        cia = data['General']['AtomPtrs'][3]
     4435        AtLookUp = G2mth.FillAtomLookUp(data['Atoms'],cia+8)
    44354436        dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
    44364437        if dlg.ShowModal() == wx.ID_OK:
  • trunk/GSASIIspc.py

    r1602 r1606  
    12831283    return KNsym[key]       
    12841284
    1285 def GetNXUPQsym(siteSym):       
    1286     'Needs a doc string'
     1285def GetNXUPQsym(siteSym):
     1286    '''       
     1287    The codes XUPQ are for lookup of symmetry constraints for position(X), thermal parm(U) & magnetic moments
     1288    (P&Q-not used in GSAS-II)
     1289    '''
    12871290    NXUPQsym = {
    12881291        '    1   ':(28,29,28,28),'   -1   ':( 1,29,28, 0),'    2(x)':(12,18,12,25),'    m(x)':(25,18,12,25),
     
    20612064        '(00g)','(1/21/2g)0q0','(1/21/2g)q00','(a00)','(a1/21/2)00q','(b1/21/2)0q0',],
    20622065#35       
    2063     'C m m 2':[],
    2064     'A 2 m m':[],
    2065     'B m 2 m':[],
     2066    'C m m 2':['(00g)','(00g)s0s','(00g)0ss','(00g)ss0','(10g)','(10g)s0s','(10g)0ss','(10g)ss0',
     2067        '(01g)','(01g)s0s','(01g)0ss','(01g)ss0','(a00)','(a00)0s0','(a01/2)','(a01/2)0s0',
     2068        '(0b0)','(0b0)s00','(0b1/2)','(0b1/2)s00',],
     2069    'A 2 m m':['(a00)','(a00)s0s','(a00)0ss','(a00)ss0','(a10)','(a10)s0s','(a10)0ss','(a10)ss0',
     2070        '(a01)','(a01)s0s','(a01)0ss','(a01)ss0','(0b0)','(0b0)00s','(1/2b0)','(1/2b0)00s',
     2071        '(00g)','(00g)0s0','(01/2g)','(01/2g)0s0',],
     2072    'B m 2 m':['(0b0)','(0b0)s0s','(0b0)0ss','(0b0)ss0','(1b0)','(1b0)s0s','(1b0)0ss','(1b0)ss0',
     2073        '(0b1)','(0b1)s0s','(0b1)0ss','(0b1)ss0','(a00)','(a00)00s','(a01/2)','(a01/2)00s',
     2074        '(00g)','(00g)s00','(1/20g)','(1/20g)s00',],
    20662075#36
    2067     'C m c 21':[],
    2068     'A 21 m a':[],
    2069     'B m 21 b':[],
    2070     'B b 21 m':[],
    2071     'C c m 21':[],
    2072     'A 21 a m':[],
     2076    'C m c 21':['(00g)','(00g)s0s','(10g)','(10g)s0s','(a00)','(a00)0s0','(0b0)','(0b0)s00',],
     2077    'A 21 m a':['(a00)','(a00)ss0','(a10)','(a10)ss0','(0b0)','(0b0)00s','(00g)','(00g)0s0',],
     2078    'B m 21 b':['(0b0)','(0b0)ss0','(1b0)','(1b0)ss0','(a00)','(a00)00s','(00g)','(00g)s00',],
     2079    'B b 21 m':['(0b0)','(0b0)0ss','(0b1)','(0b1)ss0','(a00)','(a00)00s','(00g)','(00g)s00',],
     2080    'C c m 21':['(00g)','(00g)0ss','(01g)','(01g)0ss','(a00)','(a00)0s0','(0b0)','(0b0)s00',],
     2081    'A 21 a m':['(a00)','(a00)s0s','(a01)','(a01)s0s','(0b0)','(0b0)00s','(00g)','(00g)0s0',],
    20732082#37
    2074     'C c c 2':[],
    2075     'A 2 a a':[],
    2076     'B b 2 b':[],
     2083    'C c c 2':['(00g)','(00g)s0s','(00g)0ss','(10g)','(10g)s0s','(10g)0ss','(01g)','(01g)s0s','(01g)0ss',
     2084        '(a00)','(a00)0s0','(0b0)','(0b0)s00',],
     2085    'A 2 a a':['(a00)','(a00)ss0','(a00)s0s','(a10)','(a10)ss0','(a10)ss0','(a01)','(a01)ss0','(a01)ss0',
     2086        '(0b0)','(0b0)00s','(00g)','(00g)0s0',],
     2087    'B b 2 b':['(0b0)','(0b0)0ss','(0b0)ss0','(0b1)','(0b1)0ss','(0b1)ss0','(1b0)','(1b0)0ss','(1b0)ss0',
     2088        '(a00)','(a00)00s','(00g)','(00g)s00',],
    20772089#38
    20782090    'A m m 2':[],
  • trunk/GSASIIstrMath.py

    r1604 r1606  
    15361536            refLists = Histogram['Reflection Lists']
    15371537            for phase in refLists:
     1538                if phase not in Phases:     #skips deleted or renamed phases silently!
     1539                    continue
    15381540                Phase = Phases[phase]
    15391541                im = 0
     
    15811583                    sumdF += np.abs(Fo-Fc)
    15821584                    sumdFsq += (refl[8+im]-refl[9+im])**2
    1583                 Histogram['Residuals'][phfx+'Rf'] = min(100.,(sumdF/sumFo)*100.)
    1584                 Histogram['Residuals'][phfx+'Rf^2'] = min(100.,np.sqrt(sumdFsq/sumFosq)*100.)
     1585                if sumFo:
     1586                    Histogram['Residuals'][phfx+'Rf'] = min(100.,(sumdF/sumFo)*100.)
     1587                    Histogram['Residuals'][phfx+'Rf^2'] = min(100.,np.sqrt(sumdFsq/sumFosq)*100.)
     1588                else:
     1589                    Histogram['Residuals'][phfx+'Rf'] = 100.
     1590                    Histogram['Residuals'][phfx+'Rf^2'] = 100.
    15851591                Histogram['Residuals'][phfx+'Nref'] = len(refDict['RefList'])
    15861592                Histogram['Residuals']['hId'] = hId
     
    16401646    for phase in Histogram['Reflection Lists']:
    16411647        refDict = Histogram['Reflection Lists'][phase]
     1648        if phase not in Phases:     #skips deleted or renamed phases silently!
     1649            continue
    16421650        Phase = Phases[phase]
    16431651        pId = Phase['pId']
     
    18161824    for phase in Histogram['Reflection Lists']:
    18171825        refDict = Histogram['Reflection Lists'][phase]
     1826        if phase not in Phases:     #skips deleted or renamed phases silently!
     1827            continue
    18181828        Phase = Phases[phase]
    18191829        SGData = Phase['General']['SGData']
  • trunk/imports/G2phase.py

    r1601 r1606  
    404404            elif 'spgroup' in S:
    405405                if 'X' in S:
    406                     raise self.ImportException("Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry")           
     406                    raise self.ImportException("Supersymmetry "+S+" too high; GSAS-II limited to (3+1) supersymmetry")           
    407407                SpGrp = S.split()[1]
    408408                SuperSg = ''
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