def test_combine(self):
minima = self.db.minima()
i = 5
for m1, m2 in zip(minima[:i-1], minima[1:i]):
self.connect_min(m1, m2)
for m1, m2 in zip(minima[i:], minima[i+1:]):
self.connect_min(m1, m2)
# at this point the minima should be in two disconnected groups
g = database2graph(self.db)
self.assertEqual(len(list(nx.connected_components(g))), 2)
manager = ConnectManager(self.db, strategy="combine")
m1, m2 = manager.get_connect_job()
self.connect_min(m1, m2)
# they should all be connected now
g = database2graph(self.db)
self.assertEqual(len(list(nx.connected_components(g))), 1)
def make_graph(path_to_data_dir,database):
# make a graph from the database
graph = database2graph(database)
# turn the graph into a disconnectivity graph
dg = DisconnectivityGraph(graph)
dg.calculate()
print "number of minima:", dg.tree_graph.number_of_leaves()
dg.plot()
path_to_file = os.path.join(path_to_data_dir,"Disconnectivity_graph.png")
plt.savefig(path_to_file,dpi=1000)
def test_combine(self):
minima = self.db.minima()
i = 5
for m1, m2 in zip(minima[:i - 1], minima[1:i]):
self.connect_min(m1, m2)
for m1, m2 in zip(minima[i:], minima[i + 1:]):
self.connect_min(m1, m2)
# at this point the minima should be in two disconnected groups
g = database2graph(self.db)
self.assertEqual(len(list(nx.connected_components(g))), 2)
manager = ConnectManager(self.db, strategy="combine")
m1, m2 = manager.get_connect_job()
self.connect_min(m1, m2)
# they should all be connected now
g = database2graph(self.db)
self.assertEqual(len(list(nx.connected_components(g))), 1)
def print_info(dbfname="ss60.sqlite"):
system, db = create_soft_sphere_system_from_db(dbfname)
import networkx as nx
from pele.landscape import database2graph
graph = database2graph(db)
cc = nx.connected_components(graph)
c = cc[0]
for i in range(3):
print(c[i].energy)
def print_info(dbfname="ss60.sqlite"):
system, db = create_soft_sphere_system_from_db(dbfname)
import networkx as nx
from pele.landscape import database2graph
graph = database2graph(db)
cc = nx.connected_components(graph)
c = cc[0]
for i in xrange(3):
print c[i].energy
def make_graph(database):
# make a graph from the database
graph = database2graph(database)
# turn the graph into a disconnectivity graph
dg = DisconnectivityGraph(graph,
nlevels=5,
center_gmin=False,
order_by_energy=True)
dg.calculate()
print "number of minima:", dg.tree_graph.number_of_leaves()
dg.plot()
dg.show()
if Emax is None:
Emax = -1e20
for ts in db.transition_states():
if ts.energy > Emax:
Emax = ts.energy
print 'max ts:', Emax
#check the structures with energy larger than check_e
#print paras['check_structure']
if check_structure:
for ts in db.transition_states():
if ts.energy > check_e:
print ts.coords
for rs in db.minima():
if ts.energy > check_e:
print rs.coords
graph = database2graph(db)
dg = DisconnectivityGraph(graph,
nlevels=nlevels,
Emax=Emax + 0.05,
node_offset=0)
dg.calculate()
dg.plot()
if min_state_n == 0:
dg.draw_minima([start_state], c='tab:gray')
if len(emphasize) > 0:
dg.draw_minima(emphasize, marker='o', c='tab:red')
if specified_min is not None:
dg.draw_minima([specified_min], marker='8', c='tab:green')
#find max number of atoms on surface
