def setUp(self): from pygmin.landscape import DoubleEndedConnect from pygmin.landscape._graph import create_random_database from pygmin.systems import LJCluster # from pygmin.mindist import minPermDistStochastic, MinDistWrapper # from pygmin.potentials import LJ nmin = 10 natoms=13 sys = LJCluster(natoms) pot = sys.get_potential() mindist = sys.get_mindist() db = create_random_database(nmin=nmin, natoms=natoms, nts=nmin/2) min1, min2 = list(db.minima())[:2] connect = DoubleEndedConnect(min1, min2, pot, mindist, db, use_all_min=True, merge_minima=True, max_dist_merge=1e100) self.connect = connect self.db = db self.natoms = natoms
def setUp(self): from pygmin.landscape import DoubleEndedConnect from pygmin.landscape._graph import create_random_database from pygmin.systems import LJCluster # from pygmin.mindist import minPermDistStochastic, MinDistWrapper # from pygmin.potentials import LJ nmin = 10 natoms = 13 sys = LJCluster(natoms) pot = sys.get_potential() mindist = sys.get_mindist() db = create_random_database(nmin=nmin, natoms=natoms, nts=nmin / 2) min1, min2 = list(db.minima())[:2] connect = DoubleEndedConnect(min1, min2, pot, mindist, db, use_all_min=True, merge_minima=True, max_dist_merge=1e100) self.connect = connect self.db = db self.natoms = natoms
def mytest(nmin=40, natoms=13): from pygmin.landscape import DoubleEndedConnect from pygmin.landscape._graph import create_random_database from pygmin.mindist import minPermDistStochastic, MinDistWrapper from pygmin.potentials import LJ pot = LJ() mindist = MinDistWrapper(minPermDistStochastic, permlist=[range(natoms)], niter=10) db = create_random_database(nmin=nmin, natoms=natoms) min1, min2 = list(db.minima())[:2] graph = Graph(db) connect = DoubleEndedConnect(min1, min2, pot, mindist, db, use_all_min=True, merge_minima=True, max_dist_merge=.1)
def mytest(nmin=40, natoms=13): from pygmin.landscape import DoubleEndedConnect from pygmin.landscape._graph import create_random_database from pygmin.mindist import minPermDistStochastic, MinDistWrapper from pygmin.potentials import LJ from pygmin.landscape import TSGraph pot = LJ() mindist = MinDistWrapper(minPermDistStochastic, permlist=[range(natoms)], niter=10) db = create_random_database(nmin=nmin, natoms=natoms) min1, min2 = list(db.minima())[:2] graph = TSGraph(db) connect = DoubleEndedConnect(min1, min2, pot, mindist, db, use_all_min=True, merge_minima=True, max_dist_merge=.1)