def __init__(self, lattice, model, chain_list = None, first_structure = None, temperature = 1.0):
self.lattice = lattice
self.model = model
if first_structure is None:
self.last_structure = random_avoid(self.model.natoms, self.lattice, model = model, chain_list = chain_list)
else:
self.last_structure = first_structure
self.model.calculate_energy(self.last_structure)
self.best_structure = self.last_structure
self.best_energy = self.best_structure.energy
self.mover = Reptate()
self.step = 0
if temperature > 0:
self.rt = float(temperature)
else:
raise ValueError("temperature must be > 0")
class MonteCarlo(Search):
'''Perform a Metropolis Monte Carlo search.
Parameters
----------
Required
lattice: A Lattice frombcga.lattice
model: A Model from bcga.model
Optional
termini: A list containing the indices of the ends of protein chains (only needed for multicain systems)
first_structure: A bcga.lattice_structure object to start the search (A random one will be generated if none is supplied)
temperature: The temperature used in the Metropolis test (units are dependent on the model being used)
'''
def __init__(self, lattice, model, chain_list = None, first_structure = None, temperature = 1.0):
self.lattice = lattice
self.model = model
if first_structure is None:
self.last_structure = random_avoid(self.model.natoms, self.lattice, model = model, chain_list = chain_list)
else:
self.last_structure = first_structure
self.model.calculate_energy(self.last_structure)
self.best_structure = self.last_structure
self.best_energy = self.best_structure.energy
self.mover = Reptate()
self.step = 0
if temperature > 0:
self.rt = float(temperature)
else:
raise ValueError("temperature must be > 0")
def run(self, steps):
for self.step in range (self.step +1, self.step + steps + 1):
structure = self.mover.move(self.last_structure)
energy = self.model.calculate_energy(structure)
#print self.step, structure.energy, self.last_structure.energy, self.best_structure.energy
if structure.energy < self.best_structure.energy:
self.best_structure = structure
self.best_energy = energy
if random.random() < metropolis_probability(self.last_structure.energy, structure.energy, self.rt):
self.last_structure = structure
return self.best_structure