def __init__(self, lattice, model, chain_list = None, first_structure = None):
self.lattice = lattice
self.model = model
self.step=0
if first_structure is None:
self.best_structure = random_avoid(self.model.natoms, self.lattice, model = model, chain_list = chain_list)
else:
self.best_structure =first_structure
self.best_energy = self.model.calculate_energy(self.best_structure)
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):
'''Perform a simple random search.
Parameters
----------
steps: number of structures to generate
Returns
-------
the best structure found
'''
for self.step in range (self.step +1, self.step + steps + 1):
structure=random_avoid(self.model.natoms, self.lattice, model = self.model)
energy = self.model.calculate_energy(structure)
structure.energy = energy
if energy < self.best_energy:
self.best_energy=energy
self.best_structure = structure
return self.best_structure
def test_multidomain(self):
structure=random_avoid(20, CubicLattice(), chain_list=[10,10])
self.assertEqual(0,len(structure.overlap_map))
self.assertEqual(2,structure.num_chains)
def test_trapping(self):
structure=random_avoid(150, SquareLattice())
self.assertEqual(0,len(structure.overlap_map))
def test_avoid(self):
structure=random_avoid(100, CubicLattice())
self.assertEqual(0,len(structure.overlap_map))
self.assertEqual(1,structure.num_chains)
def test_multidomain(self):
structure=random_avoid(20, CubicLattice(), chain_list=[10,10])
self.assertIsNotNone(plot_3d(structure))
self.assertIsNotNone(plot_contact_map(structure))
def test_3d(self):
structure=random_avoid(150, CubicLattice())
self.assertIsNotNone(plot_3d(structure))
def test_2d(self):
structure=random_avoid(100, SquareLattice())
self.assertIsNotNone(plot_2d(structure))
self.assertIsNotNone(plot_contact_map(structure))