def read(source_file, *args, **kwargs):
"""
Read an input file of various formats.
Arguments:
source_file:
The first argument is a structure file of some format.
The remaining args and kwargs are passed to the methods called to read the
structure.
If the structure name contains "cif" or "POSCAR" it will be read as one of
these formats. Failing that, the file is passed to the ASE read method, and
the returned Atoms object is then converted to a Structure.
Examples::
>>> io.read(INSTALL_PATH+'/io/files/POSCAR_FCC')
>>> io.read(INSTALL_PATH+'/io/files/fe3o4.cif')
"""
try:
if 'cif' in source_file:
return cif.read(source_file, *args, **kwargs)
elif ( 'POSCAR' in source_file or
'CONTCAR' in source_file ):
return poscar.read(source_file, *args, **kwargs)
else:
return ase.io.read(source_file, *args, **kwargs)
except:
try:
return poscar.read(source_file, *args, **kwargs)
except Exception:
pass
try:
return cif.read(source_file, *args, **kwargs)
except Exception:
pass
raise FormatNotSupportedError('The file %s is in an unrecognized format\
and cannot be read' % source_file)
def read(source_file, *args, **kwargs):
"""
Read an input file of various formats.
Arguments:
source_file:
The first argument is a structure file of some format.
The remaining args and kwargs are passed to the methods called to read the
structure.
If the structure name contains "cif" or "POSCAR" it will be read as one of
these formats. Failing that, the file is passed to the ASE read method, and
the returned Atoms object is then converted to a Structure.
Examples::
>>> io.read(INSTALL_PATH+'/io/files/POSCAR_FCC')
>>> io.read(INSTALL_PATH+'/io/files/fe3o4.cif')
"""
try:
if 'cif' in source_file:
return cif.read(source_file, *args, **kwargs)
elif ('POSCAR' in source_file or 'CONTCAR' in source_file):
return poscar.read(source_file, *args, **kwargs)
else:
return ase.io.read(source_file, *args, **kwargs)
except:
try:
return poscar.read(source_file, *args, **kwargs)
except Exception:
pass
try:
return cif.read(source_file, *args, **kwargs)
except Exception:
pass
raise FormatNotSupportedError('The file %s is in an unrecognized format\
and cannot be read' % source_file)
def check_POTCAR():
#=======================================================================
if __name__ == '__main__':
args= docopt(__doc__)
pitch= float(args['-p'])
leven= args['--even']
_spin_polarized= args['--spin-polarize']
_break_symmetry= args['--break-symmetry']
_metal= args['--metal']
poscar_fname= args['POSCAR']
print ' Pitch of k points = {0:5.1f}'.format(pitch)
poscar= poscar.POSCAR()
poscar.read(poscar_fname)
potcar= potcar.read_POTCAR()
species= potcar['species']
encut= max(potcar['encut'])
valences= potcar['valence']
a1= poscar.h[:,0]
a2= poscar.h[:,1]
a3= poscar.h[:,2]
al= poscar.afac
natms= poscar.num_atoms
print " species:",species
print " encut:",encut
print " valences:",valences
print " natms:",natms
ntot= 0
nele= 0
for i in range(len(natms)):
ntot= ntot +natms[i]
nele= nele +natms[i]*int(valences[i])
if _spin_polarized:
nbands= int(nele/2 *1.8)
else:
nbands= int(nele/2 *1.4)
if nbands < 50:
nbands= nele
l1= al *math.sqrt(a1[0]**2 +a1[1]**2 +a1[2]**2)
l2= al *math.sqrt(a2[0]**2 +a2[1]**2 +a2[2]**2)
l3= al *math.sqrt(a3[0]**2 +a3[1]**2 +a3[2]**2)
print ' Length of each axes:'
print ' l1 = {0:10.3f}'.format(l1)
print ' l2 = {0:10.3f}'.format(l2)
print ' l3 = {0:10.3f}'.format(l3)
k1= determine_num_kpoint(l1,pitch,leven)
k2= determine_num_kpoint(l2,pitch,leven)
k3= determine_num_kpoint(l3,pitch,leven)
print ' Number of k-points: {0:2d} {1:2d} {2:2d}'.format(k1,k2,k3)
ndiv= [k1,k2,k3]
write_KPOINTS(_KPOINTS_name,_KPOINTS_type,ndiv)
write_INCAR(_INCAR_name,encut,nbands)