def create_valid_lists(list):
point_monomer = {}
monomer_list = []
position_set = set()
for line in list:
type = line[0]
ll = np.array(line[1:]) * scale
position = tuple(ll)
m = DummyMonomer(position, type, Lattice.get_neighbours(tuple(position)))
point_monomer[position] = m
monomer_list.append(m)
position_set.add(position)
return point_monomer, monomer_list, position_set
def process(file, step=None, output_file=None):
if isinstance(file, str):
f = open(file)
else:
f = file
try:
line = f.readlines()
nr = int(line[0].replace("\n", ""))
except:
print line
sys.exit(1)
data = np.loadtxt(file, dtype=str, skiprows=1)
# data = f.readlines()[1:]
point_monomer = {}
monomer_list = []
position_set = set()
if parser.scale == -1 and "." in data[0]:
print "Atom position are float, please set -scale parameter to rescale them!"
sys.exit(1)
for line in data:
# tmp = line.replace("\n","").split(" ")
type = line[0]
ll = map(float, line[1:])
x = int(ll[0] * scale)
y = int(ll[1] * scale)
z = int(ll[2] * scale)
position = (x, y, z)
m = DummyMonomer(position, type, Lattice.get_neighbours(tuple(position)))
point_monomer[position] = m
monomer_list.append(m)
position_set.add(position)
return point_monomer, monomer_list, position_set
