def main( self ):
(opts, args) = self.parse()
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
inp = IO( opts.input,'POSCAR', "r", sysopts )
inp.read()
geom = inp.geom()
if opts.select != None:
aid = int(opts.select)
cmd = "select"
if opts.delete != None:
aid = int(opts.delete)
cmd = "delete"
# end if
atom = geom.get(aid)
atom.info()
if geom.pt == PT.Cart:
dp = geom.position( atom, PT.Direct )
cp = atom.position
else:
dp = atom.position
cp = geom.position( atom, PT.Cart )
# end if
print " Frac : %21.16f%21.16f%21.16f" % (dp[0],dp[1],dp[2])
print " Cart : %21.16f%21.16f%21.16f" % (cp[0],cp[1],cp[2])
def main( self ):
(opts, args) = self.parse()
opts_sys = { "verbose" : self.verbose, "debug" : self.debug }
try:
inp = IO( opts.input,'POSCAR', "r", opts_sys )
inp.read()
except:
if self.debug:
raise
else:
print "Input not found:", opts.input
sys.exit(1)
geom = inp.geom()
try:
band=[]
with open(opts.band) as f:
for line in f:
line = line.split()
if len(line) == 0:
continue
if line[0] == 'tot' or line[0] == 'band':
continue
# print len(line)
band.append([string.atoi(line[0]), string.atof(line[10]) ])
except:
raise
else:
print band
# sys.exit(1)
fileio = 'POSCAR'
if opts.cart:
opts_pt = { 'pt' : PT.Cart }
else:
opts_pt = { 'pt' : PT.Direct }
if opts.xyz:
opts.output += '.xyz'
fileio = 'xyz'
opts_pt = { 'pt' : PT.Cart }
else:
opts.output += '.POSCAR'
# end if
try:
out = IO( opts.output, fileio, "w+", opts_sys )
out.geom( geom )
if len(band) != 0:
out_geom = out.geom()
out_geom.band(band)
out.write( opts )
except:
if self.debug:
raise
else:
print "Output failed:", opts.output
sys.exit(1)
def main( self ):
(options, args) = self.par()
try:
atomlist = self.cfgarri( 'atomlist' )
except:
print ' Error: no atomlist'
return 0
# end try
try:
reference = self.cfg( 'reference' )
except:
reference = None
# end try
try:
origo_vec = self.cfgarrf( 'origo_vec' )
except:
origo_vec = numpy.zeros(3)
# end try
try:
vacancy = self.cfgarri( 'vacancy' )
except:
vacancy = None
# end try
try:
lat_vec = self.cfgarrf( 'lat_vec' )
except:
lat_vec = None
# end try
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = options.input_name
input_upot = IO( input_file, 'UPOT', "r", sysopts )
input_upot.read()
ref = None
if reference != None :
reference_upot = FIO( reference, 'UPOT', "r", sysopts )
reference_upot.read()
ref = reference_upot.handler
# end if
avg_cl_shift = input_upot.command( 'average', { 'atomlist' : atomlist,
'lat_vec' : lat_vec,
'origo_vec' : origo_vec,
'vacancy' : vacancy,
'reference' : ref } )
# end if
print
print ' Average Potential:', avg_cl_shift
print
def main( self ):
(options, args) = self.par()
input_name = options.input_name
output_name = options.output_name
pt = PT.Cart
if options.direct:
pt = PT.Direct
# end if
output_name += "."+PTD[pt]
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = IO( input_name,'POSCAR', "r", sysopts )
input_file.read()
geom = input_file.geom()
fileio = 'POSCAR'
opts = { 'pt' : pt }
if options.xyz:
output_name += '.xyz'
fileio = 'xyz'
opts = { 'pt' : PT.Cart }
else:
output_name += '.POSCAR'
# end if
output_file = IO( output_name,fileio, "w+", sysopts )
output_file.geom( geom )
output_file.write( opts )
def main( self ):
(options, args) = self.par()
try:
msc = self.cfgarri( 'msc' )
msc = msc.reshape([3,3])
except:
print ' Error: no supercell matrix'
return 0
# end try
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = options.input_name
input_pos = IO( input_file, 'POSCAR', "r", sysopts )
input_pos.read()
super_geom = input_pos.geom().supercell( msc )
def main( self ):
(options, args) = self.par()
input_name = options.input_name
select = int(options.select)
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
input_file = IO( input_name,'POSCAR', "r", sysopts )
input_file.read()
geom = input_file.geom()
atom = geom.get(select)
atom.info()
if geom.pt == PT.Cart:
dp = geom.position( atom, PT.Direct )
cp = atom.position
else:
dp = atom.position
cp = geom.position( atom, PT.Cart )
# end if
print " Frac : %21.16f%21.16f%21.16f" % (dp[0],dp[1],dp[2])
print " Cart : %21.16f%21.16f%21.16f" % (cp[0],cp[1],cp[2])
def main( self ):
(options, args) = self.par()
input_name = options.input_name
trans_name = options.trans_name
output_name = options.output_name
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
# read input geometry
input_file = IO( input_name, 'POSCAR', 'r', sysopts )
input_file.read()
# transform
trans_file = LX( trans_name, 'TF', sysopts )
trans_file.geom( input_file.geom() )
geom = trans_file.read()
# output
opts = { 'pt' : PT.Cart }
output_file = IO( output_name, 'POSCAR', "w+", sysopts )
output_file.geom( geom )
output_file.write( opts )
def average_upot( self, argv = None ):
atomlist = argv['atomlist']
ref = argv['reference']
vacancy = argv['vacancy']
spec = {}
avg_cl_shift = 0.000
# lattice vectors
try:
lat_vec = argv['lat_vec']
self.geom.lat_vec = numpy.reshape( lat_vec, ( 3, 3 ) )
if ref != None:
ref.geom.lat_vec = numpy.reshape( lat_vec, ( 3, 3 ) )
# end if
msg = PTD[PT.Cart]
# cart origo?
try:
origo_vec = argv['origo_vec']
except:
origo_vec = None
# end try
# end if
except:
lat_vec = None
msg = PTD[PT.Direct]
# end try
if self.verbose:
print " Coords:",msg
# end if
if lat_vec != None:
avg_xyz = Geometry()
avg_xyz.lat_vec = self.geom.lat_vec
avg_xyz.pt = PT.Cart
# end if
if self.verbose:
msg = "\n %5s %4s %12s %12s %12s %12s" % ("No","Sym","cl_shift","x","y","z")
if origo_vec != None:
msg += " %12s" % ("dr")
if ref != None:
msg += " %12s" % ("ref dr")
print msg
# end if
# cross check
if ref != None:
lookup = l_vacancy( range( 0, ref.geom.ac ), vacancy )
ref_avg_cl_shift = 0.000
# end if
for ai in atomlist:
atom = self.geom.get( ai )
s = atom.symbol
no = atom.no
cls = atom.cl_shift
pos = atom.position
avg_cl_shift += cls
# cross check
if ref != None:
ref_atom = ref.geom.get( lookup[ai] )
ref_s = ref_atom.symbol
ref_pos = ref_atom.position
ref_cls = ref_atom.cl_shift
ref_avg_cl_shift += ref_cls
# end if
# cart position
if lat_vec != None:
# change to cart
pos = self.geom.position( atom, PT.Cart )
if ref != None:
ref_pos = ref.geom.position( ref_atom, PT.Cart )
avg_xyz.add( AtomPos( s, no, cls, pos ) )
# end if
if self.verbose:
msg = " %5d %4s" % (atom.no, s)
msg += " %12.6f" % cls
msg += " %12.6f %12.6f %12.6f" % (pos[0], pos[1], pos[2])
if origo_vec != None and lat_vec != None:
msg += " %12.6f" % v_dr( origo_vec, pos )
# end if
print msg
if ref != None:
msg = "R %5d %4s" % (ref_atom.no, ref_s)
msg += " %12.6f" % ref_cls
msg += " %12.6f %12.6f %12.6f" % (ref_pos[0], ref_pos[1], ref_pos[2])
if origo_vec != None and lat_vec != None:
msg += " %12.6f" % v_dr( origo_vec, ref_pos )
msg += " %12.6f" % v_dr( ref_pos, pos )
# end if
print msg
# end if
# end if
try:
spec[s] += 1
except:
spec[s] = 1
# end try
# end for ai
if self.verbose:
print "\n Atoms: ", len( atomlist )
print " Species: ", spec
print "\n Orig. Average:", avg_cl_shift, "/", len( atomlist ), \
"=", avg_cl_shift / len( atomlist )
if ref != None:
print " Ref. Average:", ref_avg_cl_shift, "/", len( atomlist ), \
"=", ref_avg_cl_shift / len( atomlist )
print "\n Shift:", avg_cl_shift - ref_avg_cl_shift
# end if
# end if
# end if
if lat_vec != None:
avg_output = IO( 'atomlist.xyz', 'xyz', 'w+' )
avg_output.geom( avg_xyz )
avg_output.write()
# end if
avg_cl_shift /= len( atomlist )
return avg_cl_shift
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 ):
(options, args) = self.par()
input_name = options.input_name
output_name = options.output_name
ref_name = options.ref_name
ul = options.ul
ll = options.ll
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
# read input geometry
input_file = IO( input_name, 'POSCAR', 'r', sysopts )
input_file.read()
ref_file = IO( ref_name, 'POSCAR', 'r', sysopts )
ref_file.read()
# geom check
igeom = input_file.geom()
rgeom = ref_file.geom()
print "Reference: " + ref_name + " New: " + input_name
dgeom = rgeom.diff( igeom, ll, ul, options.newno )
# output
opts = { 'pt' : PT.Cart }
output_file = IO( output_name, 'diff', "w+", sysopts )
output_file.geom( dgeom )
output_file.write( opts )
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(":") )
def main( self ):
(options, args) = self.par()
input_name = options.input_name
output_name = options.output_name
diff_name = options.diff_name
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
# read input geometry
input_file = IO( input_name, 'POSCAR', 'r', sysopts )
input_file.read()
diff_file = IO( diff_name, 'diff', 'r', sysopts )
diff_file.read()
geom = input_file.geom()
dgeom = diff_file.geom()
pgeom = geom.patch( dgeom )
# output
opts = { 'pt' : PT.Cart }
output_file = IO( output_name, 'POSCAR', "w+", sysopts )
output_file.geom( pgeom )
output_file.write( opts )
def main( self ):
(opts, args) = self.parse()
opts_sys = { "verbose" : self.verbose, "debug" : self.debug }
# read input
# IO filename type mode options
try:
inp = IO( opts.input, 'POSCAR', 'r', opts_sys )
inp.read()
except:
if self.debug:
raise
else:
print "Input not found:", opts.input
sys.exit(1)
# end try
# do transformation
# LX transfile type options
try:
trs = LX( opts.trans, 'TF', opts_sys )
trs.geom( inp.geom() )
# build & process
geom = trs.read()
except:
if self.debug:
raise
else:
print "Transformation error:", opts.trans
sys.exit(1)
# end try
# write output
# IO filename type mode options
try:
out = IO( opts.output, 'POSCAR', "w+", opts_sys )
out.geom( geom )
if opts.cart:
out.write( { 'pt' : PT.Cart } )
else:
out.write( { 'pt' : PT.Direct } )
except:
if self.debug:
raise
else:
print "Output failed:", opts.output
sys.exit(1)
def main( self ):
(opts, args) = self.parse()
opts_sys = { "verbose" : self.verbose, "debug" : self.debug }
(embed,eno) = opts.embed.split( ":" )
eno = string.atoi( eno )
(host,hno) = opts.host.split( ":" )
hno = string.atoi( hno )
# read input
# IO filename type mode options
try:
embedio = IO( embed, 'POSCAR', 'r', opts_sys )
embedio.read()
except:
if self.debug:
raise
else:
print "Input not found:", embedio
sys.exit(1)
# end try
try:
hostio = IO( host, 'POSCAR', 'r', opts_sys )
hostio.read()
except:
if self.debug:
raise
else:
print "Input not found:", host
sys.exit(1)
# end try
host_geom = hostio.geom()
# where what
# self = host
host_geom.embed( hno, embedio.geom(), eno )
host_geom.normalize()
# write output
# IO filename type mode options
try:
out = IO( opts.output, 'POSCAR', "w+", opts_sys )
out.geom( host_geom )
if opts.cart:
out.write( { 'pt' : PT.Cart } )
else:
out.write( { 'pt' : PT.Direct } )
except:
if self.debug:
raise
else:
print "Output failed:", opts.output
sys.exit(1)
def main( self ):
(opts, args) = self.parse()
width = 3
sig = opts.sigma
amp = opts.amp
wsig = width * sig
sysopts = { "verbose" : self.verbose, "debug" : self.debug }
try:
inp = IO( opts.inp, 'UEIG', "r", sysopts )
inp.read()
except:
if self.debug:
raise
else:
print "Input failed:", opts.inp
sys.exit(1)
# end try
mu = 0.0
inp_ueig = inp.handler
# grid for k-point: eig occ
kp = opts.kp - 1
sp = opts.sp - 1
inp_grid = inp_ueig.grid(kp,sp)
# print inp_grid
# create input fine grid
low = inp_ueig.grid_min(kp,sp) - wsig
high = inp_ueig.grid_max(kp,sp) + wsig
#print low, high
rate = opts.rate
grid_range = high - low
maxrate = int(math.ceil( grid_range * rate ) )
# print maxrate
fine_range = np.arange( maxrate ) / float(maxrate)
# print fine_range
# shifted fine grid
inp_fine_grid = fine_range * grid_range - abs( low )
# print inp_fine_grid
# compound grid
inp_comp_grid = np.concatenate((inp_grid[:,0], inp_fine_grid))
inp_comp_grid = np.sort(inp_comp_grid)
# print inp_comp_grid
# init grid: eig, fx, d/dx fx
inp_comp_grid = np.vstack( ( inp_comp_grid,
np.zeros( len( inp_comp_grid ) ),
np.zeros( len( inp_comp_grid ) ) ) )
# print inp_comp_grid[0]
# sys.exit(0)
# generating DOS
gendos( amp, sig, inp_grid, inp_comp_grid, opts.python )
if opts.test:
sys.exit(1)
# output
out_name = opts.out + "_kp_" + str(opts.kp) + "_sp_" + str(opts.sp)
out = open( out_name , 'w')
out.write( "" )
i_range=len(inp_grid)
j_range=len(inp_comp_grid[0])
# create & write out dos
dos = np.zeros( (j_range,3) )
for j in range(0,j_range):
dos[j,0] = inp_comp_grid[0,j]
dos[j,1] = inp_comp_grid[1,j]
dos[j,2] = inp_comp_grid[2,j]
out.write( "%12.6f %12.6f %12.6f\n" % (dos[j,0],dos[j,1],dos[j,2]) )
out.close()
# dump dos
save(dos,out_name)
# plot
plot(dos)