class IO( 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
def read( self, opts = None ):
raise NotImplementedError( "read" )
# end def
### begin write
def write( self, opts = None ):
line = ["",""]
self.rewind()
self.clean()
# dump header
self.putline( self.geom.natoms() )
self.putline( self.geom.name )
try:
pt = opts['pt']
except:
pt = PT.Cart
# end try
# dump coordinates
for atom in self.geom.atoms:
s = atom.symbol
mov = atom.moveable
line[0] = " %2s" % s
# convert
pos = atom.position
if self.geom.pt != pt:
if pt == PT.Cart:
# D -> C
opos = atom.position
pos = self.geom.position_cart( atom.position )
else:
# C -> D
pos = self.geom.position_direct( atom.position )
# end if
# end if
for i in range( 0, 3 ):
line[0] += " %20.16f" % pos[i]
# end for
self.putline( line[0] )
# end for
#
self.write_buffer()
class IO( File ):
def __init__( self, path = None, opts = "", sysopts = { "verbose" : False, "debug" : False } ):
File.__init__( self, path, opts, sysopts )
self.geom = Geometry( 'POSCAR' )
self.species = {}
# end def
def read( self, opts = None ):
self.rewind()
self.clean()
self.state( 1, self.read_name )
self.state( 2, self.read_lat_c )
self.state( 3, self.read_lat_vec )
File.run( self, 3 )
self.state( 6, self.read_types )
self.state( 8, self.comment )
self.state( 9, self.read_pt )
self.state( 10, self.read_positions )
File.run( self )
self.geom.gen_species()
# self.geom.info()
# end def
### end read
def read_name( self ):
self.geom.name = ''.join( self.line() )
# end def
### begin read
def read_lat_c( self ):
constant = self.line()[0]
self.geom.lat_c = string.atof( constant )
self.process()
# end def
# super: read.lat_vec
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_pt( self ):
if string.upper( self.line()[0][0] ) == 'D':
self.geom.pt = PT.Direct
else:
self.geom.pt = PT.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, no, symb ) = self.line()
except:
( x, y, z, no, symb ) = self.line()
xm = ym = zm = 'T'
# end try
x = string.atof( x )
y = string.atof( y )
z = string.atof( z )
no = string.atoi( no )
# without renumbering
self.geom.add( AtomPos( symbol = symb, no = no,
vec = [ x, y, z ],
moveable = [ xm, ym, zm ] ), False )
if self.debug:
print " %05d Process:" % self.lc(), "%4d" % j, "%3d" % i, "%2s" % s, self.line()
# end if
j += 1
# end for
# end for
# end def
### begin write
# here we need to convert
def write( self, opts = None ):
line = ["",""]
self.rewind()
self.clean()
# dump header
self.putline( self.geom.name )
# dump lattice
self.putline( " %20.16f" % self.geom.lat_c )
for i in range( 0, 3 ):
line[0] = ""
for j in range( 0, 3 ):
line[0] += " %20.16f" % self.geom.lat_vec[i][j]
# end for
self.putline( line[0] )
# end for
# dump species
line = ["",""]
for s in self.geom.species:
line[0] += " %4s" % s
line[1] += " %4d" % self.geom.species[s]
# end for
self.putline( line[0] )
self.putline( line[1] )
# dump coordinates
self.putline( 'Selective dynamics' )
try:
pt = opts['pt']
except:
pt = PT.Direct
# end try
self.putline( PTD[ pt ] )
if self.verbose:
print " Conversion:", "%s to %s" % ( PTD[ self.geom.pt ], PTD[ pt ] )
# end if
for atom in self.geom.atoms:
line = ["",""]
# convert
pos = atom.position
if self.geom.pt != pt:
if pt == PT.Cart:
# D -> C
opos = atom.position
pos = self.geom.position_cart( atom.position )
else:
# C -> D
pos = self.geom.position_direct( atom.position )
# end if
# end if
mov = atom.moveable
for i in range( 0, 3 ):
line[0] += " %20.16f" % pos[i]
line[1] += " %2s" % TF( mov[i] )
# end for
line[0] += line[1]
line[0] += " %5d %3s" % ( atom.no, atom.symbol )
self.putline( line[0] )
# end for
#
self.putline( "" )
for atom in self.geom.atoms:
line = ""
vel = atom.velocity
for i in range( 0, 3 ):
line += " %20.16f" % vel[i]
# end for
self.putline( line )
# end for
self.write_buffer()