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)