class FileIO(File):
def __init__(self, path=None, opts="", sysopts={"verbose": False, "debug": False}):
File.__init__(self, path, opts, sysopts)
self.geom = Geometry("SCCOUT")
self.species = {}
# end def
# def read_lattice_vectors( self ):
# for i in range( 1, 4 ):
# if i > 1:
# self.getline()
# # end if
# line_arr = self.line.split()
# for j in range( 0, 3 ):
# self.geom.lattice_vectors[i-1][j] = string.atof(line_arr[j])
# # end for
# self.process()
# # end for
# # end def
def read_positions(self):
i = 1
while True:
if i > 1:
try:
self.getline()
except:
break
# end try
# end if
(no, x, y, z, r) = self.line()
x = string.atof(x)
y = string.atof(y)
z = string.atof(z)
s = self.dict["global_specie"]
atom = AtomPosition(Atom(s, i), VectorPosition([x, y, z]))
# atom.info()
self.geom.add_atom(atom)
self.process()
i += 1
# end for
self.geom.position_type = PositionTypes.Cart
# end def
def read(self, opts=None):
self.rewind()
self.clean()
self.state(2, self.read_lattice_vectors)
File.run(self, 2)
# self.state( 25, self.read_positions )
self.state(29, self.read_positions)
# self.state( 31, self.read_positions )
File.run(self)
self.geom.gen_species()
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'CHGCAR' )
self.species = {}
self._natom = 0
self.voldata = {}
self.volcol = 5
class FileIO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'xyz' )
self.species = {}
# end def
### begin write
def write( self, opts = None ):
line1 = ""
line2 = ""
self.rewind()
self.clean()
# dump header
self.putline( self.geom.number_of_atoms() )
self.putline( self.geom.name )
# dump coordinates
for a in self.geom.atoms:
s = a.symbol()
pos = a.position()
mov = a.moveable()
line1 = " %2s" % s
for i in range( 0, 3 ):
line1 += " %20.16f" % pos[i]
# end for
self.putline( line1 )
# end for
#
self.buffer_write()
def __init__(self, path=None, opts="", sysopts={"verbose": False, "debug": False}):
File.__init__(self, path, opts, sysopts)
self.geom = Geometry("SCCOUT")
self.species = {}
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'UPOT' )
self.reference_upot = None
class FileIO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'UPOT' )
self.reference_upot = None
# 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:
atom = Atom( symbol, no, cl_shift )
vpos = VectorPosition( numpy.array( [x, y, z] ) )
apos = AtomPosition( atom, vpos )
self.geom.add_atom( apos )
except Exception as ex:
print str( ex )
# self.geom.add_atom( AtomPosition( Atom( symbol, no, cl_shift ), VectorPosition( numpy.array( [x, y, z] ) ) ) )
self.process()
# end for
# 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 reference( self, argv = None ):
reference_upot = argv['reference_upot']
self.reference_upot = reference_upot
# end def
# TODO: generate atomlist with origo rmin rmax
def average_upot_on_reference( self, argv = None ):
atomlist = argv['atomlist']
if self.verbose:
print
print ' Average (reference):', atomlist
avg_cl_shift = 0.000
nat_cl_shift = 0.000
reference_geom = self.reference_upot.geom()
for i in atomlist:
reference_atom = reference_geom.get_atom( i )
nearest_atom = self.geom.nearest_atom_on_position( reference_atom.position() )
nat_cl_shift = nearest_atom.cl_shift();
if self.verbose:
rp = reference_atom.position()
np = nearest_atom.position()
dp = np - rp
dr = math.sqrt(dp[0]*dp[0]+dp[1]*dp[1]+dp[2]*dp[2])
print
print ' Reference:', "%3d" % reference_atom.no(), "%2s" % reference_atom.symbol(), rp
print ' Nearest:', "%3d" % nearest_atom.no(), "%2s" % nearest_atom.symbol(), np
print ' Distance:', dr
print ' cl shift:', nat_cl_shift
if reference_atom.symbol() != nearest_atom.symbol():
print ' WARNING: Symbol mismatch'
# end if
if dr > 0.01:
print ' WARNING: Distance to large'
# end if
# end if
avg_cl_shift += nat_cl_shift
# end for
avg_cl_shift /= len( atomlist )
return avg_cl_shift
# end def
def average_upot( self, argv = None ):
atomlist = argv['atomlist']
origo = argv['origo']
ref = argv['reference']
ono = argv['ono']
lv = argv['lv']
if lv != None:
self.geom.lattice_vectors = numpy.reshape(lv,(3,3))
if ref != None:
ref.geom.lattice_vectors = numpy.reshape(lv,(3,3))
# end if
# dump out atomlist xyz
alout = open( './atomlist.xyz', 'w' )
alout.write( str( len(atomlist) ) + "\n" )
alout.write( "\n" )
spec = {}
if self.verbose:
print
print ' Average (self): ', atomlist
avg_cl_shift = 0.000
# self
print "%5s %4s" % ("no", "sym"), "%12s %12s %12s" % ("x", "y", "z"), "%12s" % "cls", "%12s" % "dr"
for i in atomlist:
atom = self.geom.get_atom( i, True )
cls = atom.cl_shift()
avg_cl_shift += cls
s = atom.symbol()
if lv != None:
pos = self.geom.position( atom, PositionTypes.Cart )
dr = 0.000
for j in range(0,3):
dr += (origo[j] - pos[j])**2
# end for
dr = math.sqrt(dr)
else:
pos = atom.position()
print "%5d %4s" % (atom.no(), s), "%12.6f %12.6f %12.6f" % (pos[0], pos[1], pos[2]), "%12.6f" % cls, "%12.6f" % dr
try:
spec[s] += 1
except:
spec[s] = 1
mov = atom.moveable()
aline = "%2s" % s
for j in range( 0, 3 ):
aline += " %20.16f" % pos[j]
# end for
alout.write( aline + "\n" )
# end for
alout.close()
# reference cross-check
if ref != None:
ref_avg_cl_shift = 0.000
print ""
print "%5s %4s %4s" % ("no","sym","rsym"), "%12s %12s %12s" % ("dr","rdr", "ddr"), "%12s %12s %12s" % ("cls","rcls","dcls")
sd_dcls = []
for i in atomlist:
atom = self.geom.get_atom( i, True )
ii = i
if ono != None:
if i >= ono:
ii = i + 1
print ' Origo no shift: ',i,ii
ref_atom = ref.geom.get_atom( ii, True )
cls = atom.cl_shift()
ref_cls = ref_atom.cl_shift()
ref_avg_cl_shift += ref_cls
s = atom.symbol()
ref_s = ref_atom.symbol()
sd_dcls.append( cls-ref_cls )
if lv != None:
pos = self.geom.position( atom, PositionTypes.Cart )
ref_pos = self.geom.position( ref_atom, PositionTypes.Cart )
dr = 0.000
ref_dr = 0.000
for j in range(0,3):
dr += (origo[j] - pos[j])**2
ref_dr += (origo[j] - ref_pos[j])**2
# end for
dr = math.sqrt(dr)
ref_dr = math.sqrt(ref_dr)
else:
pos = atom.position()
ref_pos = ref_atom.position()
print "%5d %4s %4s" % (ref_atom.no(),s,ref_s), "%12.6f %12.6f %12.6f" % (dr,ref_dr,dr-ref_dr), "%12.6f %12.6f %12.6f" % (cls,ref_cls,cls-ref_cls)
# end for
# end if
print ""
print " Species: ", spec
print ""
print " Sum: ", avg_cl_shift," / ", len(atomlist)
avg_cl_shift /= len( atomlist )
if ref != None:
ref_avg_cl_shift /= len(atomlist)
print " Shift Mean: %12.6f" % (avg_cl_shift - ref_avg_cl_shift)
print " Shift STD: %12.6f" % numpy.std(sd_dcls)
# end if
return avg_cl_shift
# print ' Average Potential: ' + str( avg_cl_shift )
# end def
def average( self, argv = None ):
if self.reference_upot != None :
return self.average_upot_on_reference( argv )
# end if
return self.average_upot( argv )
def main( self ):
(options, args) = self.opt_parser.parse_args()
input_files_arr = {}
input_arr = {}
input_files = options.input_files
output_name = options.output_name
trans_name = options.trans_name
direct = options.direct
merge_geom = Geometry( 'Merge' )
merge_geom.position_type = PositionTypes.Cart
try:
for inp in input_files.split( "," ):
( sym, input_file ) = inp.split( ":" )
input_files_arr[sym] = input_file
# end for
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
# read inputs
for inp in input_files_arr:
sym = inp
input_file = input_files_arr[inp]
try:
input_arr[sym] = FileIO( input_file, 'SCCOUT', "r", sysopts )
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
input_arr[sym].handler.set( 'global_specie', sym )
input_arr[sym].read()
geom = input_arr[sym].geom()
geom.name = input_file
# geom.check()
try:
verbose = merge_geom.merge( geom, True, False )
if self.verbose:
print verbose
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
# end for
position_type = PositionTypes.Cart
if direct:
position_type = PositionTypes.Direct
# end if
# # merge check
# merge_geom.wignercell()
# # write out check geoms
merge_geom.order()
write_geom( output_name, sysopts, merge_geom, position_type )
try:
trans = Transform()
trans.build()
trans.process( trans_name, merge_geom )
except Exception as ex:
print str( ex )
#if self.verbose:
# raise
# end try
write_geom( output_name + ".transform", sysopts, merge_geom, position_type )
class FileIO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'POSCAR' )
self.species = {}
self.voldata = {}
# end def
### begin read
def read_lattice_constant( self ):
constant = self.line()[0]
self.geom.lattice_constant = string.atof( constant )
self.process()
self.species = {}
# end def
def read_types( self ):
line_arr_1 = self.line()
self.process()
self.getline()
line_arr_2 = self.line()
self.process()
for i in range( 0, len( line_arr_1 ) ):
self.species[line_arr_1[i]] = string.atoi( line_arr_2[i] )
# end for
# print self.species
# end def
def read_position_type( self ):
if string.upper( self.line()[0][0] ) == 'D':
self.geom.position_type = PositionTypes.Direct
else:
self.geom.position_type = PositionTypes.Cart
# end if
self.process()
# end def
# old version
def read_positions( self ):
j = 1
for s in self.species:
for i in range( 0, self.species[s] ):
if j > 1:
self.getline()
# end if
# POSCAR or CHGCAR
try:
( x, y, z, xm, ym, zm ) = self.line()
except:
( x, y, z ) = self.line()
xm = ym = zm = 'T'
# end try
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
atom = AtomPosition( Atom( s, j ), VectorPosition( [ x, y, z ], [ xm, ym, zm ] ) )
# atom.info()
self.geom.add_atom( atom )
if self.verbose:
print " %05d Process:" % self.lc(), "%4d" % j, "%3d" % i, "%2s" % s, self.line()
# end if
j += 1
# end for
# end for
# end def
# converter version
# do not need to convert at read
def new_bad_read_positions( self, position_type = PositionTypes.Direct ):
j = 1
for s in self.species:
for i in range( 0, self.species[s] ):
if j > 1:
self.getline()
# end if
try:
( x, y, z, xm, ym, zm ) = self.line()
except:
( x, y, z ) = self.line()
xm = ym = zm = 'T'
# end try
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
pos = numpy.zeros( 3 )
convert = 'O'
# convert
if self.geom.position_type != position_type:
if position_type == PositionTypes.Cart:
# D -> C
convert = 'D->C'
rho = numpy.array( [ x, y, z ] )
pos = self.geom.position_cart( rho )
else:
# C -> D
convert = 'C->D'
r = numpy.array( [ x, y, z ] )
pos = self.geom.position_direct( r )
# end if
else:
pos = numpy.array( [x, y, z ] )
# end if
# atom = AtomPosition( Atom( s, j ), VectorPosition( [ x, y, z ], [ xm, ym, zm ] ) )
atom = AtomPosition( Atom( s, j ), VectorPosition( pos, numpy.array( [ xm, ym, zm ] ) ) )
# print [x,y,z]
# print pos
# atom.info()
self.geom.add_atom( atom )
if self.verbose:
print " %05d Process:" % self.lc(), "%4d" % j, "%3d" % i, "%2s" % s, self.line(), "%5s" % convert
# end if
j += 1
# end for
# end for
# end def
def read( self, opts = None ):
self.rewind()
self.clean()
self.state( 1, self.comment )
self.state( 2, self.read_lattice_constant )
self.state( 3, self.read_lattice_vectors )
File.run( self, 3 )
self.state( 6, self.read_types )
self.state( 8, self.comment )
self.state( 9, self.read_position_type )
# self.state( 8, self.read_position_type )
self.state( 10, self.read_positions )
File.run( self )
self.geom.gen_species()
self.geom.check()
# end def
### end read
### begin write
# here we need to convert
def write( self, opts = None ):
line1 = ""
line2 = ""
self.rewind()
self.clean()
# dump header
self.putline( self.geom.name )
# dump lattice
self.putline( " %20.16f" % self.geom.lattice_constant )
for i in range( 0, 3 ):
line1 = ""
for j in range( 0, 3 ):
line1 += " %20.16f" % self.geom.lattice_vectors[i][j]
# end for
self.putline( line1 )
# end for
# dump species
line1 = ""
line2 = ""
for s in self.geom.species:
line1 += " %4s" % s
line2 += " %4d" % self.geom.species[s]
# end for
self.putline( line1 )
self.putline( line2 )
# dump coordinates
self.putline( 'Selective dynamics' )
try:
position_type = opts['position_type']
except:
position_type = PositionTypes.Direct
# end try
# self.putline( PositionTypesDict[ self.geom.position_type ] )
self.putline( PositionTypesDict[ position_type ] )
# print self.geom.position_type
# print position_type
if self.verbose:
print " Conversion:", "%s to %s" % ( PositionTypesDict[ self.geom.position_type ], PositionTypesDict[ position_type ] )
# end if
for a in self.geom.atoms:
line1 = ""
line2 = ""
# convert
if self.geom.position_type != position_type:
if position_type == PositionTypes.Cart:
# D -> C
opos = a.position()
pos = self.geom.position_cart( a.position() )
else:
# C -> D
pos = self.geom.position_direct( a.position() )
# end if
else:
pos = a.position()
# end if
mov = a.moveable()
for i in range( 0, 3 ):
line1 += " %20.16f" % pos[i]
line2 += " %2s" % TF( mov[i] )
# end for
line1 += line2
self.putline( line1 )
# end for
#
self.putline( "" )
for a in self.geom.atoms:
line1 = ""
vel = a.velocity()
for i in range( 0, 3 ):
line1 += " %20.16f" % vel[i]
# end for
self.putline( line1 )
# end for
# print self.buffer.lines
self.buffer_write()
class FileIO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'CHGCAR' )
self.species = {}
self._natom = 0
self.voldata = {}
self.volcol = 5
# end def
### begin read
def read_lattice_constant( self ):
constant = self.line()[0]
self.geom.lattice_constant = string.atof( constant )
self.process()
self.species = {}
self.ngx = 0
self.ngy = 0
self.ngz = 0
# end def
def read_types( self ):
line_arr_1 = self.line()
self.process()
self.getline()
line_arr_2 = self.line()
self.process()
self._natom
for i in range( 0, len( line_arr_1 ) ):
sna = string.atoi( line_arr_2[i] )
self._natom += sna
self.species[line_arr_1[i]] = sna
# end for
# print self.species
# end def
def read_position_type( self ):
if string.upper( self.line()[0][0] ) == 'D':
self.geom.position_type = PositionTypes.Direct
else:
self.geom.position_type = PositionTypes.Cart
# end if
self.process()
# end def
def read_gdim( self ):
(ngx,ngy,ngz) = self.line()
self.ngx = string.atoi( ngx )
self.ngy = string.atoi( ngy )
self.ngz = string.atoi( ngz )
# self.ng = ngx * ngy * ngz
if self.verbose:
print " %05d Process:" % self.lc(), self.line()
# end if
# end def
def ng( self ):
return self.ngx * self.ngy * self.ngz
# end def
# old version
def read_positions( self ):
j = 1
for s in self.species:
for i in range( 0, self.species[s] ):
if j > 1:
self.getline()
# end if
( x, y, z ) = self.line()
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
atom = AtomPosition( Atom( s, j ), VectorPosition( [ x, y, z ] ) )
# atom.info()
self.geom.add_atom( atom )
if self.verbose:
print " %05d Process:" % self.lc(), "%4d" % j, "%3d" % i, "%2s" % s, self.line()
# end if
j += 1
# end for
# end for
# end def
def read_voldata( self ):
# allocate
# data lines
dle = int(math.floor( self.ng() / self.volcol )) + 1
self.voldata['total'] = numpy.zeros(self.ng())
print " L: ",dle," S:",self.ng()
j = 1
ik = 0
# dle
for i in range(0,dle):
if j > 1:
self.getline()
# endif
larr = self.line()
for k in range(0,self.volcol):
try:
self.voldata['total'][ik] = string.atof(larr[k])
except Exception as ex:
pass
ik += 1
# end for
# print " %05d Process:" % self.lc(), ik
j += 1
# end for
# end def
def add( self, argv = {} ):
s = argv['s']
a = argv['a']
b = argv['b']
mv = self.voldata['total']
sv = s.voldata()
sv = sv['total']
dv = a * mv + b * sv
self.voldata['diff'] = dv
# end def
def read( self, opts = None ):
self.rewind()
self.clean()
self.state( 1, self.comment )
self.state( 2, self.read_lattice_constant )
self.state( 3, self.read_lattice_vectors )
File.run( self, 3 )
self.state( 6, self.read_types )
# self.state( 8, self.comment )
self.state( 8, self.read_position_type )
self.state( 9, self.read_positions )
File.run( self, 9 )
eor = 9 + self._natom + 1
self.state( eor , self.read_gdim )
File.run( self, eor )
self.state( eor + 1 , self.read_voldata )
File.run( self )
self.geom.gen_species()
# self.geom.check()
# print self.voldata
# end def
### end read
### begin write
# here we need to convert
def write( self, opts = None ):
line1 = ""
line2 = ""
self.rewind()
self.clean()
# dump header
self.putline( self.geom.name )
# dump lattice
self.putline( " %20.16f" % self.geom.lattice_constant )
for i in range( 0, 3 ):
line1 = ""
for j in range( 0, 3 ):
line1 += " %20.16f" % self.geom.lattice_vectors[i][j]
# end for
self.putline( line1 )
# end for
# dump species
line1 = ""
line2 = ""
for s in self.geom.species:
line1 += " %4s" % s
line2 += " %4d" % self.geom.species[s]
# end for
self.putline( line1 )
self.putline( line2 )
# dump coordinates
# self.putline( 'Selective dynamics' )
try:
position_type = opts['position_type']
except:
position_type = PositionTypes.Direct
# end try
# self.putline( PositionTypesDict[ self.geom.position_type ] )
self.putline( PositionTypesDict[ position_type ] )
# print self.geom.position_type
# print position_type
if self.verbose:
print " Conversion:", "%s to %s" % ( PositionTypesDict[ self.geom.position_type ], PositionTypesDict[ position_type ] )
# end if
for a in self.geom.atoms:
line1 = ""
line2 = ""
# convert
if self.geom.position_type != position_type:
if position_type == PositionTypes.Cart:
# D -> C
opos = a.position()
pos = self.geom.position_cart( a.position() )
else:
# C -> D
pos = self.geom.position_direct( a.position() )
# end if
else:
pos = a.position()
# end if
mov = a.moveable()
for i in range( 0, 3 ):
line1 += " %20.16f" % pos[i]
# line2 += " %2s" % TF( mov[i] )
# end for
#line1 += line2
self.putline( line1 )
# end for
#
self.putline( "" )
# for a in self.geom.atoms:
# line1 = ""
# vel = a.velocity()
# for i in range( 0, 3 ):
# line1 += " %20.16f" % vel[i]
# # end for
# self.putline( line1 )
# # end for
# # print self.buffer.lines
self.putline( "%5d %5d %5d" % ( self.ngx, self.ngy, self.ngz ) )
if opts['diff']:
vd = self.voldata['diff']
else:
vd = self.voldata['total']
# end if
line1 = ""
vc = 0
for v in vd:
vc += 1
line1 += " %20.16f" % v
if vc % 5:
vc = 1
self.putline( line1 )
line1 = ""
# end for
if vc > 1:
self.putline( line1 )
self.buffer_write()
