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)