class TestDistanceGraph(unittest.TestCase):
def setUp(self):
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]
self.db = db
self.natoms = natoms
self.connect = DoubleEndedConnect(min1, min2, pot, mindist, db,
merge_minima=True, max_dist_merge=1e100)
# for ts in db.transition_states():
# self.add_ts(ts.energy, ts.coords,
# ts.minimum1.energy, ts.minimum1.coords,
# ts.minimum2.energy, ts.minimum2.coords)
for m in db.minima():
self.connect.dist_graph.addMinimum(m)
def make_result(self, coords, energy):
from pele.optimize import Result
res = Result()
res.coords = coords
res.energy = energy
res.eigenval = 1.
res.eigenvec = coords.copy()
return res
def add_ts(self, tse, tsx, m1e, m1x, m2e, m2x):
tsres = self.make_result(tsx, tse)
min_ret1 = self.make_result(m1x, m1e)
min_ret2 = self.make_result(m2x, m2e)
return self.connect._addTransitionState(tsres, min_ret1, min_ret2)
def test_merge_minima(self):
"""merge two minima and make sure the distance graph is still ok"""
min3, min4 = list(self.db.minima())[2:4]
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
print min3._id, min4._id, "are connected", self.connect.graph.areConnected(min3, min4)
print min3._id, "number of edges", self.connect.graph.graph.degree(min3)
print min4._id, "number of edges", self.connect.graph.graph.degree(min4)
self.connect.mergeMinima(min3, min4)
self.assertNotIn(min4, self.connect.graph.graph)
self.assertNotIn(min4, self.connect.dist_graph.Gdist)
self.assertNotIn(min4, self.db.minima())
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "merging broke the distance graph")
def test_add_TS_existing_minima(self):
from pele.optimize import Result
min3, min4 = list(self.db.minima())[4:6]
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
print min3._id, min4._id, "are connected", self.connect.graph.areConnected(min3, min4)
print min3._id, "number of edges", self.connect.graph.graph.degree(min3)
print min4._id, "number of edges", self.connect.graph.graph.degree(min4)
coords = np.random.uniform(-1,1,self.natoms*3)
E = float(min3.energy + min4.energy)
tsres = self.make_result(coords, E)
min_ret1 = self.make_result(min3.coords, min3.energy)
min_ret2 = self.make_result(min4.coords, min4.energy)
self.connect._addTransitionState(tsres, min_ret1, min_ret2)
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding a transition state broke the distance graph")
def test_add_TS_new_minima(self):
min3 = list(self.db.minima())[6]
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
# print min3._id, min4._id, "are connected", self.connect.graph.areConnected(min3, min4)
print min3._id, "number of edges", self.connect.graph.graph.degree(min3)
#create new minimum from thin air
coords = np.random.uniform(-1,1,self.natoms*3)
E = np.random.rand()*10.
min_ret1 = self.make_result(min3.coords, min3.energy)
min_ret2 = self.make_result(coords, E)
# min_ret2 = [coords, E]
# min_ret1 = [min3.coords, min3.energy]
#create new TS from thin air
coords = np.random.uniform(-1,1,self.natoms*3)
E = float(min3.energy + min_ret2.energy)
tsres = self.make_result(coords, E)
self.connect._addTransitionState(tsres, min_ret1, min_ret2)
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding a transition state broke the distance graph")
def run_add_TS(self, min3, min4, nocheck=False):
if not nocheck:
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
print min3._id, min4._id, "are connected", self.connect.graph.areConnected(min3, min4)
print min3._id, "number of edges", self.connect.graph.graph.degree(min3)
print min4._id, "number of edges", self.connect.graph.graph.degree(min4)
coords = np.random.uniform(-1,1,self.natoms*3)
E = float(min3.energy + min4.energy)
tsres = self.make_result(coords, E)
min_ret1 = self.make_result(min3.coords, min3.energy)
min_ret2 = self.make_result(min4.coords, min4.energy)
# min_ret1 = [min3.coords, min3.energy]
# min_ret2 = [min4.coords, min4.energy]
self.connect._addTransitionState(tsres, min_ret1, min_ret2)
if not nocheck:
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding a transition state broke the distance graph")
def test_add_TS_existing_not_connected(self):
minima = list(self.db.minima())
min3 = minima[2]
for min4 in minima[3:]:
if not self.connect.graph.areConnected(min3, min4):
break
self.run_add_TS(min3, min4)
def test_add_TS_existing_already_connected(self):
minima = list(self.db.minima())
min3 = minima[2]
for min4 in minima[3:]:
if self.connect.graph.areConnected(min3, min4):
break
self.run_add_TS(min3, min4)
def test_add_TS_multiple(self):
minima = list(self.db.minima())
min3 = minima[2]
nnew = 4
for min4 in minima[3:3+nnew]:
self.run_add_TS(min3, min4, nocheck=True)
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding multiple transition states broke the distance graph")
class TestDistanceGraph(unittest.TestCase):
def setUp(self):
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]
self.db = db
self.natoms = natoms
self.connect = DoubleEndedConnect(min1, min2, pot, mindist, db,
merge_minima=True, max_dist_merge=1e100)
# for ts in db.transition_states():
# self.add_ts(ts.energy, ts.coords,
# ts.minimum1.energy, ts.minimum1.coords,
# ts.minimum2.energy, ts.minimum2.coords)
for m in db.minima():
self.connect.dist_graph.addMinimum(m)
def make_result(self, coords, energy):
from pele.optimize import Result
res = Result()
res.coords = coords
res.energy = energy
res.eigenval = 1.
res.eigenvec = coords.copy()
return res
def add_ts(self, tse, tsx, m1e, m1x, m2e, m2x):
tsres = self.make_result(tsx, tse)
min_ret1 = self.make_result(m1x, m1e)
min_ret2 = self.make_result(m2x, m2e)
return self.connect._addTransitionState(tsres, min_ret1, min_ret2)
def test_merge_minima(self):
# merge two minima and make sure the distance graph is still ok
min3, min4 = list(self.db.minima())[2:4]
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
print min3.id(), min4.id(), "are connected", self.connect.graph.areConnected(min3, min4)
print min3.id(), "number of edges", self.connect.graph.graph.degree(min3)
print min4.id(), "number of edges", self.connect.graph.graph.degree(min4)
self.connect.mergeMinima(min3, min4)
self.assertNotIn(min4, self.connect.graph.graph)
self.assertNotIn(min4, self.connect.dist_graph.Gdist)
self.assertNotIn(min4, self.db.minima())
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "merging broke the distance graph")
def test_add_TS_existing_minima(self):
min3, min4 = list(self.db.minima())[4:6]
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
print min3.id(), min4.id(), "are connected", self.connect.graph.areConnected(min3, min4)
print min3.id(), "number of edges", self.connect.graph.graph.degree(min3)
print min4.id(), "number of edges", self.connect.graph.graph.degree(min4)
coords = np.random.uniform(-1,1,self.natoms*3)
E = float(min3.energy + min4.energy)
tsres = self.make_result(coords, E)
min_ret1 = self.make_result(min3.coords, min3.energy)
min_ret2 = self.make_result(min4.coords, min4.energy)
self.connect._addTransitionState(tsres, min_ret1, min_ret2)
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding a transition state broke the distance graph")
def test_add_TS_new_minima(self):
min3 = list(self.db.minima())[6]
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
# print min3.id(), min4.id(), "are connected", self.connect.graph.areConnected(min3, min4)
print min3.id(), "number of edges", self.connect.graph.graph.degree(min3)
#create new minimum from thin air
coords = np.random.uniform(-1,1,self.natoms*3)
E = np.random.rand()*10.
min_ret1 = self.make_result(min3.coords, min3.energy)
min_ret2 = self.make_result(coords, E)
# min_ret2 = [coords, E]
# min_ret1 = [min3.coords, min3.energy]
#create new TS from thin air
coords = np.random.uniform(-1,1,self.natoms*3)
E = float(min3.energy + min_ret2.energy)
tsres = self.make_result(coords, E)
self.connect._addTransitionState(tsres, min_ret1, min_ret2)
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding a transition state broke the distance graph")
def run_add_TS(self, min3, min4, nocheck=False):
if not nocheck:
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "the distance graph is broken at the start")
print min3.id(), min4.id(), "are connected", self.connect.graph.areConnected(min3, min4)
print min3.id(), "number of edges", self.connect.graph.graph.degree(min3)
print min4.id(), "number of edges", self.connect.graph.graph.degree(min4)
coords = np.random.uniform(-1,1,self.natoms*3)
E = float(min3.energy + min4.energy)
tsres = self.make_result(coords, E)
min_ret1 = self.make_result(min3.coords, min3.energy)
min_ret2 = self.make_result(min4.coords, min4.energy)
# min_ret1 = [min3.coords, min3.energy]
# min_ret2 = [min4.coords, min4.energy]
self.connect._addTransitionState(tsres, min_ret1, min_ret2)
if not nocheck:
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding a transition state broke the distance graph")
def test_add_TS_existing_not_connected(self):
minima = list(self.db.minima())
min3 = minima[2]
for min4 in minima[3:]:
if not self.connect.graph.areConnected(min3, min4):
break
self.run_add_TS(min3, min4)
def test_add_TS_existing_already_connected(self):
minima = list(self.db.minima())
min3 = minima[2]
for min4 in minima[3:]:
if self.connect.graph.areConnected(min3, min4):
break
self.run_add_TS(min3, min4)
def test_add_TS_multiple(self):
minima = list(self.db.minima())
min3 = minima[2]
nnew = 4
for min4 in minima[3:3+nnew]:
self.run_add_TS(min3, min4, nocheck=True)
allok = self.connect.dist_graph.checkGraph()
self.assertTrue(allok, "adding multiple transition states broke the distance graph")
