from lj_run import LJClusterNew
import sys
from pele.landscape import Graph
natoms = int(sys.argv[1])
dbname = sys.argv[2]
system = LJClusterNew(natoms)
db = system.create_database(dbname)
while True:
min1 = db.minima()[0]
graph = Graph(db)
all_connected = True
for m2 in db.minima()[1:]:
if not graph.areConnected(min1, m2):
all_connected = False
break
if all_connected:
print "minima are all connected, ending"
exit(1)
connect = system.get_double_ended_connect(min1, m2, db, fresh_connect=True, load_no_distances=True)
connect.connect()
for i in range(len(configs)):
if np.random.uniform(0, 1) < prob:
x, energy = self.get_starting_configuration_minima(Emax)
configs[i] = Replica(x, energy, from_random=False)
if self.verbose:
print "sampling from minima, E minimum:", energy, "with probability:", prob
return configs
if __name__ == "__main__":
# define the system
from lj_run import LJClusterNew
natoms = 13
system = LJClusterNew(natoms)
db = system.create_database("lj%d.db" % (natoms))
# if True:
# populate_database(system, db, niter=100)
print "pgorder", db.minima()[0].pgorder
print "fvib", db.minima()[0].fvib
get_thermodynamic_information(system, db)
print "pgorder", db.minima()[0].pgorder
print "fvib", db.minima()[0].fvib
Emin = db.minima()[0].energy
Emax = Emin + 1.
k = system.k
for i in range(10):
coords, E = sample_from_database(system, db, Emax)
import numpy as np
from lj_run import LJClusterNew
from pygmin.takestep import RandomDisplacement, AdaptiveStepsize, Reseeding
if __name__ == "__main__":
natoms = 75
system = LJClusterNew(natoms)
ts = RandomDisplacement(stepsize=0.42)
takestep = AdaptiveStepsize(ts)
takestep = Reseeding(takestep,system.get_random_configuration(),maxnoimprove=80)
label = "lj%d" % (natoms)
dbname = label + ".db"
db = system.create_database(dbname)
bh = system.get_basinhopping(database=db, takestep=ts, temperature=0.45, insert_rejected=True)
bh.run(1000000)
prob = onset_prob / float(self.nreplicas)
for i in range(len(configs)):
if np.random.uniform(0,1) < prob:
x, energy = self.get_starting_configuration_minima(Emax)
configs[i] = Replica(x, energy, from_random=False)
if self.verbose:
print "sampling from minima, E minimum:", energy, "with probability:", prob
return configs
if __name__ == "__main__":
# define the system
from lj_run import LJClusterNew
natoms = 13
system = LJClusterNew(natoms)
db = system.create_database("lj%d.db" % (natoms))
# if True:
# populate_database(system, db, niter=100)
print "pgorder", db.minima()[0].pgorder
print "fvib", db.minima()[0].fvib
get_thermodynamic_information(system, db)
print "pgorder", db.minima()[0].pgorder
print "fvib", db.minima()[0].fvib
Emin = db.minima()[0].energy
Emax = Emin + 1.
k = system.k
for i in range(10):
coords, E = sample_from_database(system, db, Emax)
