def write_geom( name = "output", sysopts = { "verbose" : False, "debug" : False }, geom = None, position_type = PositionTypes.Cart ):
output = FileIO( name + ".xyz",'xyz', "w+", sysopts )
output.geom( geom )
output.write()
output = FileIO( name + ".POSCAR",'POSCAR', "w+", sysopts )
output.geom( geom )
output.write( { "position_type" : position_type } )
def main( self ):
(options, args) = self.opt_parser.parse_args()
input_name = options.input_name
output_name = options.output_name
direct = options.direct
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
try:
input_file = FileIO( input_name,'POSCAR', "r", sysopts )
except Exception as ex:
print 'Error: ' + str( ex )
# end try
input_file.read()
geom = input_file.geom()
# geom.check()
position_type = PositionTypes.Cart
if direct:
position_type = PositionTypes.Direct
# end if
try:
output_file = FileIO( output_name,'POSCAR', "w+", sysopts )
output_file.geom( geom )
output_file.write( { 'position_type' : position_type } )
except Exception as ex:
print 'Error: ' + str( ex )
def main( self ):
(options, args) = self.opt_parser.parse_args()
direct = options.direct
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_desc = options.input_desc
(input_file,input_sym,input_no) = input_desc.split( ":" )
input_no = string.atoi( input_no )
embed_desc = options.embed_desc
(embed_file,embed_sym,embed_no) = embed_desc.split( ":" )
embed_no = string.atoi( embed_no )
try:
input_poscar = FileIO( input_file, 'POSCAR', "r", sysopts )
embed_poscar = FileIO( embed_file, 'POSCAR', "r", sysopts )
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
input_poscar.read()
embed_poscar.read()
geom = input_poscar.geom()
geom.embed( embed_poscar.geom(), embed_sym, embed_no, input_sym, input_no )
geom.gen_species()
geom.order()
position_type = PositionTypes.Cart
if direct:
position_type = PositionTypes.Direct
# end if
write_geom( 'embed', sysopts, geom, position_type )
def main( self ):
(options, args) = self.opt_parser.parse_args()
try:
sigma = self.getoptf( 'sigma' )
except:
sigma = 0.100
# end try
try:
alpha = self.getoptf( 'alpha' )
except:
alpha = 2.000
# end try
try:
kpt = self.getoptf( 'kpt' )
except:
kpt = 1
# end try
try:
channels = self.getopti( 'channels' )
except:
channels = 2048
# end try
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = options.input_file
try:
input_ueig = FileIO( input_file, 'UEIG', "r", sysopts )
except:
if self.debug:
raise
print ' Error: ' + input_file
return 0
# end try
input_ueig.read()
# print input_ueig.handler.ibuffer.lines
avg_cl_shift = input_ueig.command( 'gendos', { 'sigma' : sigma,
'alpha' : alpha,
'kpt' : kpt,
'channels' : channels} )
def main( self ):
(opts, args) = self.parse()
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
a = string.atof(opts.amin)
b = string.atof(opts.bsub)
# read inputs
min_file = FileIO( opts.min_name, 'CHGCAR', "r", sysopts )
min_file.read()
sub_file = FileIO( opts.sub_name, 'CHGCAR', "r", sysopts )
sub_file.read()
min_file.command('add', { 's': sub_file, 'a' : a, 'b' : b} )
min_file.handler.path = 'diff.CHGCAR'
min_file.handler.opts = 'w+'
min_file.handler.buffer = min_file.handler.obuffer
min_file.write( { 'diff' : True } )
def main( self ):
(options, args) = self.opt_parser.parse_args()
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = options.input_file
try:
input_dat = FileIO( input_file, 'dat', "r", sysopts )
except:
if self.debug:
raise
print ' Error: ' + input_file
return 0
# end try
input_dat.read()
avg_cl_shift = input_dat.command( 'average' )
# end if
print
print ' Average Potential (line):', avg_cl_shift
print
def main( self ):
(options, args) = self.opt_parser.parse_args()
input_name = options.input_name
output_name = options.output_name
trans_name = options.trans_name
direct = options.direct
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
# position type
position_type = PositionTypes.Cart
if direct:
position_type = PositionTypes.Direct
# end if
# read inputs
try:
input_file = FileIO( input_name, 'POSCAR', "r", sysopts )
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
input_file.read()
geom = input_file.geom()
try:
trans = Transform()
trans.build()
trans.process( trans_name, geom )
except Exception as ex:
print ' No transformation: ' + str( ex )
if self.verbose:
raise
# end try
geom.gen_species()
geom.order()
write_geom( output_name, sysopts, geom, position_type )
def main( self ):
(options, args) = self.opt_parser.parse_args()
try:
atomlist = self.getoptarri( 'atomlist' )
except:
print ' Error: no atomlist'
return 0
# end try
# print atomlist
try:
reference = self.getopt( 'reference' )
except:
reference = None
# end try
try:
origo = self.getoptarrf( 'origo' )
except:
origo = nump.zero(3)
# end try
try:
ono = self.getopti( 'ono' )
except:
ono = None
# end try
try:
lv = self.getoptarrf( 'lv' )
except:
lv = None
# end try
try:
rmin = self.getoptf( 'rmin' )
except:
rmin = None
# end try
try:
rmax = self.getoptf( 'rmax' )
except:
rmax = None
# end try
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = options.input_file
try:
input_upot = FileIO( input_file, 'UPOT', "r", sysopts )
except:
if self.debug:
raise
print ' Error: ' + input_file
return 0
# end try
if reference != None :
try:
reference_upot = FileIO( reference, 'UPOT', "r", sysopts )
reference_upot.read()
except:
if self.debug:
raise
print ' Error: ' + reference
return 0
# end try
# end if
input_upot.read()
# if reference != None:
# input_upot.command( 'reference', { 'reference_upot' : reference_upot } )
# # end if
if reference != None:
ref = reference_upot.handler
else:
ref = None
# end if
avg_cl_shift = input_upot.command( 'average', { 'atomlist' : atomlist,
'lv' : lv,
'origo' : origo,
'reference' : ref,
'ono' : ono } )
# end if
print
print ' Average Potential:', avg_cl_shift
print
def main( self ):
(options, args) = self.opt_parser.parse_args()
try:
scale = self.getoptarri( 'scale' )
except:
print ' Error: no scale'
return 0
# end try
try:
shift = self.getoptarrf( 'shift' )
except:
shift = numpy.zeros( 3 )
# end try
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = options.input_file
try:
input_poscar = FileIO( input_file, 'POSCAR', "r", sysopts )
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
input_poscar.read()
geom = input_poscar.geom()
for s in geom.species:
output_file = str( s ) + "-" + input_file + ".wsgen"
# print output_file
try:
output_in = open( output_file, "w+" )
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
output_in.write( "transformation\n" )
output_in.write( "%9.6f %9.6f %9.6f\n" % (scale[0], 0.000000, 0.000000) )
output_in.write( "%9.6f %9.6f %9.6f\n" % (0.000000, scale[1], 0.000000) )
output_in.write( "%9.6f %9.6f %9.6f\n" % (0.000000, 0.000000, scale[2]) )
output_in.write( "userdef\n" )
for lv in geom.lattice_vectors:
output_in.write( "%20.16f %20.16f %20.16f\n" % (lv[0], lv[1], lv[2]) )
# end for
output_in.write( "%d\n" % geom.species[s] )
# find specie s
for atom in geom.atoms:
if atom.symbol() == s:
pos = geom.position( atom, PositionTypes.Cart )
output_in.write( "%20.16f %20.16f %20.16f\n" % (pos[0], pos[1], pos[2]) )
# end if
# end for
output_in.write( "\n%20.16f %20.16f %20.16f\n" % (shift[0], shift[1], shift[2]) )
output_in.close()
# end for s
# check geom
output_file = "primitive.xyz"
try:
output_xyz = open( output_file, "w+" )
except Exception as ex:
print ' Error: ' + str( ex )
return 0
# end try
output_xyz.write( "%d\n\n" % geom.number_of_atoms() )
for s in geom.species:
for atom in geom.atoms:
if atom.symbol() == s:
pos = geom.position( atom, PositionTypes.Cart )
output_xyz.write( "%2s %20.16f %20.16f %20.16f\n" % (s, pos[0], pos[1], pos[2]) )
# end if
# end for
# end for
output_xyz.close()