def average_upot( self, argv = None ):
atomlist = argv['atomlist']
ref = argv['reference']
vacancy = argv['vacancy']
spec = {}
avg_cl_shift = 0.000
# lattice vectors
try:
lat_vec = argv['lat_vec']
self.geom.lat_vec = numpy.reshape( lat_vec, ( 3, 3 ) )
if ref != None:
ref.geom.lat_vec = numpy.reshape( lat_vec, ( 3, 3 ) )
# end if
msg = PTD[PT.Cart]
# cart origo?
try:
origo_vec = argv['origo_vec']
except:
origo_vec = None
# end try
# end if
except:
lat_vec = None
msg = PTD[PT.Direct]
# end try
if self.verbose:
print " Coords:",msg
# end if
if lat_vec != None:
avg_xyz = Geometry()
avg_xyz.lat_vec = self.geom.lat_vec
avg_xyz.pt = PT.Cart
# end if
if self.verbose:
msg = "\n %5s %4s %12s %12s %12s %12s" % ("No","Sym","cl_shift","x","y","z")
if origo_vec != None:
msg += " %12s" % ("dr")
if ref != None:
msg += " %12s" % ("ref dr")
print msg
# end if
# cross check
if ref != None:
lookup = l_vacancy( range( 0, ref.geom.ac ), vacancy )
ref_avg_cl_shift = 0.000
# end if
for ai in atomlist:
atom = self.geom.get( ai )
s = atom.symbol
no = atom.no
cls = atom.cl_shift
pos = atom.position
avg_cl_shift += cls
# cross check
if ref != None:
ref_atom = ref.geom.get( lookup[ai] )
ref_s = ref_atom.symbol
ref_pos = ref_atom.position
ref_cls = ref_atom.cl_shift
ref_avg_cl_shift += ref_cls
# end if
# cart position
if lat_vec != None:
# change to cart
pos = self.geom.position( atom, PT.Cart )
if ref != None:
ref_pos = ref.geom.position( ref_atom, PT.Cart )
avg_xyz.add( AtomPos( s, no, cls, pos ) )
# end if
if self.verbose:
msg = " %5d %4s" % (atom.no, s)
msg += " %12.6f" % cls
msg += " %12.6f %12.6f %12.6f" % (pos[0], pos[1], pos[2])
if origo_vec != None and lat_vec != None:
msg += " %12.6f" % v_dr( origo_vec, pos )
# end if
print msg
if ref != None:
msg = "R %5d %4s" % (ref_atom.no, ref_s)
msg += " %12.6f" % ref_cls
msg += " %12.6f %12.6f %12.6f" % (ref_pos[0], ref_pos[1], ref_pos[2])
if origo_vec != None and lat_vec != None:
msg += " %12.6f" % v_dr( origo_vec, ref_pos )
msg += " %12.6f" % v_dr( ref_pos, pos )
# end if
print msg
# end if
# end if
try:
spec[s] += 1
except:
spec[s] = 1
# end try
# end for ai
if self.verbose:
print "\n Atoms: ", len( atomlist )
print " Species: ", spec
print "\n Orig. Average:", avg_cl_shift, "/", len( atomlist ), \
"=", avg_cl_shift / len( atomlist )
if ref != None:
print " Ref. Average:", ref_avg_cl_shift, "/", len( atomlist ), \
"=", ref_avg_cl_shift / len( atomlist )
print "\n Shift:", avg_cl_shift - ref_avg_cl_shift
# end if
# end if
# end if
if lat_vec != None:
avg_output = IO( 'atomlist.xyz', 'xyz', 'w+' )
avg_output.geom( avg_xyz )
avg_output.write()
# end if
avg_cl_shift /= len( atomlist )
return avg_cl_shift
