def prepare_system(self, frozen_atoms=None):
if not frozen_atoms: frozen_atoms = [0, 2, 4]
self.natoms = 13
fsys = LJCluster(self.natoms)
self.reference_coords = fsys.get_random_configuration()
self.system = LJClusterFrozen(self.natoms, frozen_atoms, self.reference_coords)
def prepare_system(self, frozen_atoms=[0, 2, 4]):
self.natoms = 13
fsys = LJCluster(self.natoms)
self.reference_coords = fsys.get_random_configuration()
self.system = LJClusterFrozen(self.natoms, frozen_atoms, self.reference_coords)
class TestLJCluster(unittest.TestCase):
def setUp(self):
self.prepare_system(frozen_atoms=[0, 2, 4, 6])
def prepare_system(self, frozen_atoms=None):
if not frozen_atoms: frozen_atoms = [0, 2, 4]
self.natoms = 13
fsys = LJCluster(self.natoms)
self.reference_coords = fsys.get_random_configuration()
self.system = LJClusterFrozen(self.natoms, frozen_atoms,
self.reference_coords)
def make_database(self, nminima=2):
db = self.system.create_database()
bh = self.system.get_basinhopping(db)
while db.number_of_minima() < 2:
bh.run(1)
return db
def test1(self):
coords = self.system.coords_converter.get_reduced_coords(
self.reference_coords)
pot = self.system.get_potential()
pot.getEnergy(coords)
def test_mobile(self):
self.assertEqual(3 * self.system.nmobile,
self.system.coords_converter.get_mobile_dof().size)
def testpermlist(self):
permlist = self.system.get_permlist()
self.assertEqual(len(permlist[0]),
self.natoms - len(self.system.frozen_atoms))
def test_basinhopping(self):
db = self.system.create_database()
bh = self.system.get_basinhopping(db)
while db.number_of_minima() < 2:
bh.run(1)
def test_connect(self):
db = self.make_database()
min1, min2 = db.minima()[:2]
connect = self.system.get_double_ended_connect(min1, min2, db)
connect.connect()
# self.assertTrue(connect.success())
def test_fvib(self):
db = self.make_database()
get_thermodynamic_information(self.system, db, nproc=1)
class TestLJCluster(unittest.TestCase):
def setUp(self):
self.prepare_system(frozen_atoms=[0, 2, 4, 6])
def prepare_system(self, frozen_atoms=None):
if not frozen_atoms: frozen_atoms = [0, 2, 4]
self.natoms = 13
fsys = LJCluster(self.natoms)
self.reference_coords = fsys.get_random_configuration()
self.system = LJClusterFrozen(self.natoms, frozen_atoms, self.reference_coords)
def make_database(self, nminima=2):
db = self.system.create_database()
bh = self.system.get_basinhopping(db)
while db.number_of_minima() < 2:
bh.run(1)
return db
def test1(self):
coords = self.system.coords_converter.get_reduced_coords(self.reference_coords)
pot = self.system.get_potential()
pot.getEnergy(coords)
def test_mobile(self):
self.assertEqual(3 * self.system.nmobile, self.system.coords_converter.get_mobile_dof().size)
def testpermlist(self):
permlist = self.system.get_permlist()
self.assertEqual(len(permlist[0]), self.natoms - len(self.system.frozen_atoms))
def test_basinhopping(self):
db = self.system.create_database()
bh = self.system.get_basinhopping(db)
while db.number_of_minima() < 2:
bh.run(1)
def test_connect(self):
db = self.make_database()
min1, min2 = db.minima()[:2]
connect = self.system.get_double_ended_connect(min1, min2, db)
connect.connect()
# self.assertTrue(connect.success())
def test_fvib(self):
db = self.make_database()
get_thermodynamic_information(self.system, db, nproc=1)
