class IO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'ASEPOT' )
self.reference = None
# end def
def read( self, opts = None ):
self.rewind()
self.clean()
self.state( 1, self.comment )
self.state( 2, self.read_types_header )
self.state( 3, self.comment )
self.state( 4, self.read_types )
File.run( self, 4 )
self.state( 4 + self.types, self.comment )
self.state( 4 + self.types + 2, self.comment )
self.state( 4 + self.types + 3, self.read_lat_c )
self.state( 4 + self.types + 4, self.read_lat_vec )
self.state( 4 + self.types + 8, self.read_ions )
File.run( self )
self.geom.gen_species()
# end def
def read_types_header( self ):
(types,ions) = self.line()
self.types = string.atoi( types )
self.ions = string.atoi( ions )
self.process()
# end def
def read_types( self ):
for i in range( 1, self.types + 1 ):
if i > 1:
self.getline()
# end if
self.process()
# end for
# end def
def read_ions( self ):
for i in range( 1, self.ions + 1 ):
if i > 1:
self.getline()
# end if
(no,symbol,cl_shift,x,y,z) = self.line()
no = string.atoi( no )
# VMD indexes
no = no - 1
cl_shift = string.atof( cl_shift )
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
try:
self.geom.add( AtomPos( symbol, no, cl_shift, numpy.array( [x, y, z] ) ) )
except Exception as ex:
print str( ex )
# end try
self.process()
# end for
# end def
def read_lat_c( self ):
constant = self.line()[0]
self.geom.lat_c = string.atof( constant )
self.process()
# end def
# super: read_lat_vec
# PRB 78, 235104-5 (7)
# EPA(D,q) = q * (V_Dq - V_H)
# shift = (inp - ref)
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
# end def
def compare( self, complist = None, eps = 0.01 ):
shift = 0.00000
one = 1.000000
zero = 0.000000
c = 0
ref = self.geom
inp = self.geom.geom
for k,v in complist.iteritems():
k = int(k)
v = int(v)
ratom = ref.get(k)
rpos = ratom.position
rcls = ratom.cl_shift
iatom = inp.get(v)
ipos = iatom.position
icls = iatom.cl_shift
if ratom.symbol != iatom.symbol:
raise Warning( "Symbol mismatch!" )
# G2012-04-12
# normalize coordinates
for i in range(0,3):
if ipos[i] > one:
ipos[i] -= one
if abs(one - ipos[i]) < eps:
ipos[i] = one - ipos[i]
if rpos[i] > one:
rpos[i] -= one
if abs(one - rpos[i]) < eps:
rpos[i] = one - rpos[i]
# end for
print "REF %4d %2s %12.9f %12.9f %12.9f %12.9f" % (ratom.no,ratom.symbol,rpos[0],rpos[1],rpos[2],rcls)
print "INP %4d %2s %12.9f %12.9f %12.9f %12.9f" % (iatom.no,iatom.symbol,ipos[0],ipos[1],ipos[2],icls)
print "L2 INP-REF: %12.9f" %(l2norm(ipos-rpos))
print
# print ratom.no,ratom.symbol,ratom.position
# print iatom.no,iatom.symbol,iatom.position
shift += icls - rcls
c += 1
# end for
print "Shift:",shift/float(c)
print
# end def
def ino( self, no, vl ):
vl.sort()
for i in vl:
if no >= i:
no = no - 1
# end for
return no
# end def
def average( self, vaclist = None ):
shift = 0.00000
one = 1.000000
zero = 0.000000
c = 0
inp = self.geom
ref = self.geom.geom
# for crop check
crop = self.geom.clone()
err_symbol = {}
err_dist = {}
for aref in ref.atoms:
# reference
rno = aref.rno
rpos = aref.position
rcls = aref.cl_shift
# input
ino = self.ino( rno, vaclist )
if(ino!=rno):
print "INDEX SHIFT: %d -> %d" %(rno,ino)
ainp = inp.get(ino)
ipos = ainp.position
icls = ainp.cl_shift
crop.add(ainp)
if aref.symbol != ainp.symbol:
raise Warning( "Symbol mismatch!" )
err_symbol[rno] = ino
# end if
# G2012-04-12
# normalize coordinates
ipos = rcnorm( ipos, 0.01 )
rpos = rcnorm( rpos, 0.01 )
dist = l2norm(ipos-rpos)
ps = icls-rcls
print "REF %4d %2s %12.9f %12.9f %12.9f %12.9f" % (rno,aref.symbol,rpos[0],rpos[1],rpos[2],rcls)
print "INP %4d %2s %12.9f %12.9f %12.9f %12.9f" % (ainp.no,ainp.symbol,ipos[0],ipos[1],ipos[2],icls)
if(dist > 0.05):
print "HIGH DISTANCE"
err_dist[rno] = ino
# end if
print "L2(INP-REF) %12.9f Shift %12.9f" %(dist,ps)
print "ASEDIFF %4d %2s %12.9f %12.9f" %(rno,aref.symbol,aref.dist,ps)
print
shift += ps
c += 1
# end for
if len(err_symbol):
print
print "Symbol mismatch"
for k,v in err_symbol.iteritems():
rno=int(k)
ino=int(v)
aref=ref.get(rno)
ainp=inp.get(ino)
rpos=aref.position
ipos=ainp.position
rcls = aref.cl_shift
icls = ainp.cl_shift
print "ERR SYMB REF %4d %2s %12.9f %12.9f %12.9f %12.9f" % (rno,aref.symbol,rpos[0],rpos[1],rpos[2],rcls)
print "ERR SYMB INP %4d %2s %12.9f %12.9f %12.9f %12.9f" % (ino,ainp.symbol,ipos[0],ipos[1],ipos[2],icls)
print
# end for
# end if
if len(err_dist):
print
print "High distance"
for k,v in err_symbol.iteritems():
rno=int(k)
ino=int(v)
aref=ref.get(rno)
ainp=inp.get(ino)
rpos=aref.position
ipos=ainp.position
rcls = aref.cl_shift
icls = ainp.cl_shift
print "ERR DIST REF %4d %2s %12.9f %12.9f %12.9f %12.9f" % (rno,aref.symbol,rpos[0],rpos[1],rpos[2],rcls)
print "ERR DIST INP %4d %2s %12.9f %12.9f %12.9f %12.9f" % (ino,ainp.symbol,ipos[0],ipos[1],ipos[2],icls)
print
# end for
# end if
print "APS %4d %12.9f" % ( c, shift/float(c) )
print
crop.normalize()
#crop.info()
return crop
# end def
# end class
class IO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'UPOT' )
self.reference = None
# end def
def read( self, opts = None ):
self.rewind()
self.clean()
self.state( 1, self.comment )
self.state( 2, self.read_types_header )
self.state( 3, self.comment )
self.state( 4, self.read_types )
File.run( self, 4 )
self.state( 4 + self.types, self.comment )
self.state( 4 + self.types + 2, self.comment )
self.state( 4 + self.types + 3, self.read_ions )
File.run( self )
self.geom.gen_species()
# self.geom.check()
# end def
def read_types_header( self ):
(types,ions) = self.line()
self.types = string.atoi( types )
self.ions = string.atoi( ions )
self.process()
# end def
def read_types( self ):
for i in range( 1, self.types + 1 ):
if i > 1:
self.getline()
# end if
self.process()
# end for
# end def
def read_ions( self ):
for i in range( 1, self.ions + 1 ):
if i > 1:
self.getline()
# end if
(no,symbol,cl_shift,x,y,z) = self.line()
no = string.atoi( no )
cl_shift = string.atof( cl_shift )
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
try:
self.geom.add( AtomPos( symbol, no, cl_shift, numpy.array( [x, y, z] ) ) )
except Exception as ex:
print str( ex )
# end try
self.process()
# end for
# end def
# PRB 78, 235104-5 (7)
# EPA(D,q) = q * (V_Dq - V_H)
# shift = (inp - ref)
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
# end def
def compare( self, complist = None, eps = 0.01 ):
shift = 0.00000
one = 1.000000
zero = 0.000000
c = 0
ref = self.geom
inp = self.geom.geom
for k,v in complist.iteritems():
k = int(k)
v = int(v)
ratom = ref.get(k)
rpos = ratom.position
rcls = ratom.cl_shift
iatom = inp.get(v)
ipos = iatom.position
icls = iatom.cl_shift
if ratom.symbol != iatom.symbol:
raise Warning( "Symbol mismatch!" )
# G2012-04-12
# normalize coordinates
for i in range(0,3):
if ipos[i] > one:
ipos[i] -= one
if abs(one - ipos[i]) < eps:
ipos[i] = one - ipos[i]
if rpos[i] > one:
rpos[i] -= one
if abs(one - rpos[i]) < eps:
rpos[i] = one - rpos[i]
# end for
print "REF %4d %2s %12.9f %12.9f %12.9f %12.9f" % (ratom.no,ratom.symbol,rpos[0],rpos[1],rpos[2],rcls)
print "INP %4d %2s %12.9f %12.9f %12.9f %12.9f" % (iatom.no,iatom.symbol,ipos[0],ipos[1],ipos[2],icls)
print "L2 INP-REF: %12.9f" %(l2norm(ipos-rpos))
print
# print ratom.no,ratom.symbol,ratom.position
# print iatom.no,iatom.symbol,iatom.position
shift += icls - rcls
c += 1
# end for
print "Shift:",shift/float(c)
print
# def
def average( self, atomlist = None ):
shift = 0.00000
c = 0
ref = self.geom
inp = self.geom.geom
for i in atomlist:
i = int(i)
ratom = ref.get( i )
rpos = ratom.position
rcls = ratom.cl_shift
j = ref.geom_match[i]
iatom = inp.get( j )
ipos = iatom.position
icls = iatom.cl_shift
if ratom.symbol != iatom.symbol:
raise Warning( "Symbol mismatch!" )
print "REF %4d %2s %12.9f %12.9f %12.9f %12.9f" % (ratom.no,ratom.symbol,rpos[0],rpos[1],rpos[2],rcls)
print "INP %4d %2s %12.9f %12.9f %12.9f %12.9f" % (iatom.no,iatom.symbol,ipos[0],ipos[1],ipos[2],icls)
# print ratom.no,ratom.symbol,ratom.position
# print iatom.no,iatom.symbol,iatom.position
shift += icls - rcls
c += 1
# end for
print "Shift:",shift/float(c)
print
class IO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'UPOT' )
self.reference = None
# end def
def read( self, opts = None ):
self.rewind()
self.clean()
self.state( 1, self.comment )
self.state( 2, self.read_types_header )
self.state( 3, self.comment )
self.state( 4, self.read_types )
File.run( self, 4 )
self.state( 4 + self.types, self.comment )
self.state( 4 + self.types + 2, self.comment )
self.state( 4 + self.types + 3, self.read_ions )
File.run( self )
self.geom.gen_species()
# self.geom.check()
# end def
def read_types_header( self ):
(types,ions) = self.line()
self.types = string.atoi( types )
self.ions = string.atoi( ions )
self.process()
# end def
def read_types( self ):
for i in range( 1, self.types + 1 ):
if i > 1:
self.getline()
# end if
self.process()
# end for
# end def
def read_ions( self ):
for i in range( 1, self.ions + 1 ):
if i > 1:
self.getline()
# end if
(no,symbol,cl_shift,x,y,z) = self.line()
no = string.atoi( no )
cl_shift = string.atof( cl_shift )
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
try:
self.geom.add( AtomPos( symbol, no, cl_shift, numpy.array( [x, y, z] ) ) )
except Exception as ex:
print str( ex )
# end try
self.process()
# end for
# end def
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
# end def
def average( self, argv = None ):
return self.average_upot( argv )