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()