def test2(self):
from pele.storage import Database
from pele.systems import LJCluster
np.random.seed(0)
natoms = 13
system = LJCluster(natoms)
pot = system.get_potential()
mindist = system.get_mindist(niter=1)
db = Database()
db.addMinimum(pot.getEnergy(_x1), _x1)
db.addMinimum(pot.getEnergy(_x2), _x2)
m1, m2 = db.minima()
connect = DoubleEndedConnect(m1, m2, pot, mindist, db, verbosity=10)
connect.connect()
self.assertTrue(connect.success())
path = connect.returnPath()
if (myconnect.graph.areConnected(min1, min2)):
print "ALERT: The minima are already connected in the database file", dbfile
print " Delete it for a fresh run."
myconnect.connect()
print ""
print "found a path!"
#the path is now saved in the database. Lets retrieve it and
#print it in a more visual format
#now retrieve the path for printing
print ""
mints, S, energies = myconnect.returnPath()
nmin = (len(mints)-1)/2 + 1
nts = nmin-1
print "the path has %d minima and %d transition states" % (nmin, nts)
eofs = "path.EofS"
print "saving energies to", eofs
with open(eofs, "w") as fout:
for i in range(len(S)):
fout.write("%f %f\n" % (S[i], energies[i]))
xyzfile = "path.xyz"
print "saving path in xyz format to", xyzfile
with open(xyzfile, "w") as fout:
for m in mints:
write_xyz(fout, m.coords, title=str(m.energy))
if (myconnect.graph.areConnected(min1, min2)):
print "ALERT: The minima are already connected in the database file", dbfile
print " Delete it for a fresh run."
myconnect.connect()
print ""
print "found a path!"
# the path is now saved in the database. Lets retrieve it and
# print it in a more visual format
# now retrieve the path for printing
print ""
mints, S, energies = myconnect.returnPath()
nmin = (len(mints) - 1) / 2 + 1
nts = nmin - 1
print "the path has %d minima and %d transition states" % (nmin, nts)
eofs = "path.EofS"
print "saving energies to", eofs
with open(eofs, "w") as fout:
for i in range(len(S)):
fout.write("%f %f\n" % (S[i], energies[i]))
xyzfile = "path.xyz"
print "saving path in xyz format to", xyzfile
with open(xyzfile, "w") as fout:
for m in mints:
write_xyz(fout, m.coords, title=str(m.energy))
