def position_sort(self, coordinate="z", height=None, symbol=None):
col = {"x": 0, "y": 1, "z": 2}
pos = geomread(self.posfile).get_positions()
data = list()
for i in range(len(self.atom_list)):
atom = self.atom_list[i] + str(i)
charge = self.bader_charges[atom]
data.append([atom, pos[i, 0], pos[i, 1], pos[i, 2], charge])
index = col[coordinate] + 1
data = sorted(data, key=lambda t: t[index])
# for dat in data:
# print dat
# for i in range(len(data)-1):
# print '%-10s%-10s%10.5f%10.5f%10.5f' % (data[i][0], data[i+1][0], data[i+1][3], data[i][3], data[i+1][3] - data[i][3])
info = list()
if (height) and (symbol):
for i in range(len(data)):
if (symbol in data[i][0]) and (data[i][3] >= height):
# print data[i][0], data[i][3]
print data[i]
info.append([data[i][1], data[i][2], data[i][4]])
else:
print "nice try!"
info = np.array(info)
print info
for i in range(len(info)):
print info[i, 0], info[i, 1]
return info
def __init__(self, restart=False, chgcar="CHGCAR", chgcarsum="CHGCARsum", posfile="POSCAR", datafile="ACF.dat"):
self.restart = restart
self.chgcar = chgcar
self.chgcarsum = chgcarsum
self.posfile = posfile
self.datafile = datafile
# self.atom_list = list()
self.atom_list = geomread(self.posfile).get_atom_list()
self.bader_charges = dict()
def __init__(self, dosfile='DOSCAR', posfile='POSCAR', status='r'):
DensityOfStates.__init__(self, dosfile=dosfile, posfile=posfile, status=status)
# print 'Doscar.__init__() called'
if (posfile is None):
posfile = 'POSCAR'
try:
pos = geomread(posfile)
self.set_atom_types(pos.get_atom_list())
except IOError:
print 'POSCAR file %s cannot be found. Atoms types are set to default.' % poscar
if (status == 'r'):
self.read_dosfile(dosfile)
def __init__(self, chgfile='CHGCAR', posfile='POSCAR', status='r'):
ChargeDensity.__init__(self, chgfile=chgfile, status=status)
pos = geomread(posfile)
self.atomlist = pos.get_atom_list()
self.coordinates = pos.get_positions()
