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 copy_config(self, config):
array_to_pos(self.lmp, config)
