def __init__(self, lmp_, input_file_=None):
self.num_atoms = lmp_.extract_global("natoms", 0)
self.num_atom_types = []
self.atom_types = []
self.initial_positions = pos_to_array(lmp_)
self.positions_store = pos_to_array(lmp_)
self.positions = pos_to_array(lmp_)
if input_file_ == None:
print "No input file defined in atoms system"
exit()
else:
"""
Assign atom types.
"""
data_file = get_data_file(input_file_)
print "Obtaining atom types from " + data_file
with open(data_file) as f:
content = f.readlines()
types_array = get_atom_types(input_file_)
self.num_atom_types = int(str.split(content[3])[0])
print str(self.num_atom_types) + " found of type:"
print types_array
for i in range(self.num_atoms):
atom_type = int(
str.split(content[14 + (self.num_atom_types) + i])[1])
self.atom_types.append(types_array[atom_type - 1])
print "Atom types are as follows:"
print self.atom_types
print "\n"
def __init__(self, lmp_, input_file_ = None):
self.num_atoms = lmp_.extract_global("natoms", 0)
self.num_atom_types = []
self.atom_types = []
self.initial_positions = pos_to_array(lmp_)
self.positions_store = pos_to_array(lmp_)
self.positions = pos_to_array(lmp_)
if input_file_ == None:
print "No input file defined in atoms system"
exit()
else:
"""
Assign atom types.
"""
data_file = get_data_file(input_file_)
print "Obtaining atom types from " + data_file
with open(data_file) as f:
content = f.readlines()
types_array=get_atom_types(input_file_)
self.num_atom_types = int(str.split(content[3])[0])
print str(self.num_atom_types) + " found of type:"
print types_array
for i in range(self.num_atoms):
atom_type = int(str.split(content[14+(self.num_atom_types)+i])[1])
self.atom_types.append(types_array[atom_type-1])
print "Atom types are as follows:"
print self.atom_types
print "\n"
def assign_atom_types(self, input_file_):
"""
Assign atom types.
"""
data_file = get_data_file(input_file_)
print "Obtaining atom types from " + data_file
with open(data_file) as f:
content = f.readlines()
types_array=get_atom_types(input_file_)
self.num_atom_types = int(str.split(content[3])[0])
print str(self.num_atom_types) + " found of type:"
print types_array
for i in range(self.num_atoms):
atom_type = int(str.split(content[14+(self.num_atom_types)+i])[1])
self.atom_types.append(types_array[atom_type-1])
print "Atom types are as follows:"
print self.atom_types
print "\n"
def assign_atom_types(self, input_file_):
"""
Assign atom types.
"""
data_file = get_data_file(input_file_)
print "Obtaining atom types from " + data_file
with open(data_file) as f:
content = f.readlines()
types_array = get_atom_types(input_file_)
self.num_atom_types = int(str.split(content[3])[0])
print str(self.num_atom_types) + " found of type:"
print types_array
for i in range(self.num_atoms):
atom_type = int(
str.split(content[14 + (self.num_atom_types) + i])[1])
self.atom_types.append(types_array[atom_type - 1])
print "Atom types are as follows:"
print self.atom_types
print "\n"