def main( self ):
(opts, args) = self.parse()
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
### begin reference
try:
print opts.reference,":"
ref = IO( opts.reference, 'UPOT', "r", sysopts )
ref.read()
except:
if self.debug:
raise
else:
print "Reference failed:", opts.reference
sys.exit(1)
# end try
# set geoms
gref = ref.geom()
# check furthest in reference
if not opts.max == None:
(origo,max) = opts.max.split(":")
origo = int(origo)
max = float(max)
gref.furthest( origo, max )
return
# end if
### end reference
### begin input
try:
inp = IO( opts.input, 'UPOT', "r", sysopts )
print opts.input,":"
inp.read()
except:
if self.debug:
raise
else:
print "Input failed:", opts.input
sys.exit(1)
# end try
gref.geom = inp.geom()
### end input
if not opts.compare == None:
complist = {}
pairs = opts.compare.split(",")
for p in pairs:
(k,v) = p.split(":")
complist[k] = v
# end for
print
ref.compare( complist )
return
# end if
# warning: geoms should have the same lattice
# generate match table
if not opts.match == None:
if not opts.cache == None:
match = open( opts.cache, 'wb' )
# end if
gref.match( opts.match )
# write out match cache
if not opts.cache == None:
pickle.dump(gref.geom_match,match,-1)
return
# end if
# end if
if not opts.average == None:
if not opts.cache == None:
match = open( opts.cache, 'rb' )
gref.geom_match = pickle.load( match )
match.close()
else:
raise Exception( "Cache error" )
# end if
print
ref.average( opts.average.split(":") )
def main( self ):
(opts, args) = self.parse()
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
### begin reference
try:
print opts.reference,":"
ref = IO( opts.reference, 'ASEPOT', "r", sysopts )
ref.read()
except:
if self.debug:
raise
else:
print "Reference failed:", opts.reference
sys.exit(1)
# end try
# set geoms
gref = ref.geom()
if opts.poscar:
out = IO( 'vsasepot.ref.POSCAR', 'POSCAR', "w+", sysopts )
out.geom( gref )
out.write()
# end if
# G2012-04-27
if not opts.origo == None:
gref.shift_origo(opts.origo)
# end if
# check furthest in reference
if not opts.rho == None:
rho = float( opts.rho )
crop = gref.cart_select( rho )
if crop.ac == 0:
print "EMPTY SELECTION, SET SMALLER RHO"
sys.exit(1)
out = 'ref.crop.POSCAR'
out = IO( out, 'POSCAR', "w+", sysopts )
out.geom( crop )
out.write()
# for atom in crop.atoms:
# atom.info()
# # end for
# end if
### end reference
### begin input
try:
inp = IO( opts.input, 'ASEPOT', "r", sysopts )
print opts.input,":"
inp.read()
except:
if self.debug:
raise
else:
print "Input failed:", opts.input
sys.exit(1)
# end try
igeom = inp.geom()
igeom.geom = crop
### end input
if not opts.vacancy == None:
vaclist = opts.vacancy.split(",")
for i in range(0,len(vaclist)):
vaclist[i] = int(vaclist[i])
# end for
crop = inp.average( vaclist )
out = 'inp.crop.POSCAR'
out = IO( out, 'POSCAR', "w+", sysopts )
out.geom( crop )
out.write()
return
# end if
if not opts.compare == None:
complist = {}
pairs = opts.compare.split(",")
for p in pairs:
(k,v) = p.split(":")
complist[k] = v
# end for
print
ref.compare( complist )
return
# end if
# warning: geoms should have the same lattice
# generate match table
if not opts.match == None:
if not opts.cache == None:
match = open( opts.cache, 'wb' )
# end if
gref.match( opts.match )
# write out match cache
if not opts.cache == None:
pickle.dump(gref.geom_match,match,-1)
return
# end if
# end if
if not opts.average == None:
if not opts.cache == None:
match = open( opts.cache, 'rb' )
gref.geom_match = pickle.load( match )
match.close()
else:
raise Exception( "Cache error" )
# end if
print
ref.average( opts.average.split(":") )