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 generate_configuration(self,
lmp_,
radius_,
lower_bound_=float('-inf'),
upper_bound_=float('inf'),
moves_=1000):
"""
Generate an initial configuration that lies within an energy range.
"""
# Function shortcuts for speed.
move = self.move_atom
pick_atom = self.get_random_atom
# Initialise lammps for initial input.
lmp_.command("run 0 post no")
lmp_.command("variable e equal pe")
# Extract the atomic coordinates.
# This is an array of pointers.
# Note: Changing these values will alter the values in lammps.
self.positions = lmp_.extract_atom("x", 3)
# Calculate and store the total energy of the initial configuration.
lmp_.command("variable elast equal $e")
elast = lmp_.extract_variable("elast", None, 0)
# Store previous positions.
self.positions_store = pos_to_array(lmp_)
for i in xrange(1, moves_):
# Move all atoms
# Gibbs sampler (all atoms are moved)
for j in xrange(self.num_atoms):
# Move selected atom to generate a new configuration.
move(j, radius_)
# Run lammps for the new configuration.
lmp_.command("run 0 post no")
# Refresh positions from lammps.
# Required due to book-keeping (neighbour lists etc).
self.positions = lmp_.extract_atom("x", 3)
# Extract the total energy of the new configuration.
lmp_.command("variable enew equal v_e")
enew = lmp_.extract_variable("enew", None, 0)
# Apply WL criterion to see if the move is accepted.
if enew < upper_bound_ and enew > lower_bound_:
# print "Found initial configuration."
# print "Energy of initial configuration = " + str(enew)
return 1. / float(i)
else:
# If the move is rejected revert to original position of atom.
array_to_pos(lmp_, self.positions_store)
array_to_pos(lmp_, self.positions_store)
lmp_.command("run 0 post no")
def generate_configuration(self, lmp_, radius_,lower_bound_=float('-inf'),
upper_bound_=float('inf'), moves_ = 1000):
"""
Generate an initial configuration that lies within an energy range.
"""
# Function shortcuts for speed.
move = self.move_atom
pick_atom = self.get_random_atom
# Initialise lammps for initial input.
lmp_.command("run 0 post no")
lmp_.command("variable e equal pe")
# Extract the atomic coordinates.
# This is an array of pointers.
# Note: Changing these values will alter the values in lammps.
self.positions = lmp_.extract_atom("x", 3)
# Calculate and store the total energy of the initial configuration.
lmp_.command("variable elast equal $e")
elast = lmp_.extract_variable("elast", None, 0)
# Store previous positions.
self.positions_store = pos_to_array(lmp_)
for i in xrange(1, moves_):
# Move all atoms
# Gibbs sampler (all atoms are moved)
for j in xrange(self.num_atoms):
# Move selected atom to generate a new configuration.
move(j, radius_)
# Run lammps for the new configuration.
lmp_.command("run 0 post no")
# Refresh positions from lammps.
# Required due to book-keeping (neighbour lists etc).
self.positions = lmp_.extract_atom("x", 3)
# Extract the total energy of the new configuration.
lmp_.command("variable enew equal v_e")
enew = lmp_.extract_variable("enew", None, 0)
# Apply WL criterion to see if the move is accepted.
if enew < upper_bound_ and enew > lower_bound_:
# print "Found initial configuration."
# print "Energy of initial configuration = " + str(enew)
return 1./float(i)
else:
# If the move is rejected revert to original position of atom.
array_to_pos(lmp_,self.positions_store)
array_to_pos(lmp_,self.positions_store)
lmp_.command("run 0 post no")
def get_config(self):
return pos_to_array(self.lmp)