def test1(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(
db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin=os.path.join(current_dir, "points.min"),
pointsts=os.path.join(current_dir, "points.ts"),
endianness="<")
converter.convert()
mdata = tempfile.NamedTemporaryFile(delete=True)
tsdata = tempfile.NamedTemporaryFile(delete=True)
pm = tempfile.NamedTemporaryFile(delete=True)
pts = tempfile.NamedTemporaryFile(delete=True)
print mdata.name, tsdata.name
writer = WritePathsampleDB(db,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
writer.write_db()
d1 = np.genfromtxt(os.path.join(current_dir, "min.data"))[:, :3]
d2 = np.genfromtxt(mdata.name)[:, :3]
_base_test.assert_arrays_almost_equal(self, d1, d2)
d1 = np.genfromtxt(os.path.join(current_dir,
"ts.data")).reshape(-1, 8)[:, :5]
d2 = np.genfromtxt(tsdata.name).reshape(-1, 8)[:, :5]
print d1, d2
_base_test.assert_arrays_almost_equal(self, d1, d2)
self.assertEqual(sha1_of_file(os.path.join(current_dir, "points.min")),
sha1_of_file(pm.name))
self.assertEqual(sha1_of_file(os.path.join(current_dir, "points.ts")),
sha1_of_file(pts.name))
def test2(self):
from pele.utils.tests.test_disconnectivity_graph import create_random_database
db = create_random_database(nmin=20, nts=15)
delete = False
mdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".min.data")
tsdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".ts.data")
pm = tempfile.NamedTemporaryFile(delete=delete)
pts = tempfile.NamedTemporaryFile(delete=delete)
print mdata.name, tsdata.name
writer = WritePathsampleDB(db,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
writer.write_db()
newdb = Database()
reader = OptimDBConverter(newdb,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
reader.convert()
for m1, m2 in izip(db.minima(), newdb.minima()):
self.assertAlmostEqual(m1.energy, m2.energy)
_base_test.assert_arrays_almost_equal(self, m1.coords, m2.coords)
for ts1, ts2 in izip(db.transition_states(),
newdb.transition_states()):
self.assertAlmostEqual(ts1.energy, ts2.energy)
_base_test.assert_arrays_almost_equal(self, ts1.coords, ts2.coords)
self.assertAlmostEqual(ts1.minimum1.energy, ts2.minimum1.energy)
self.assertAlmostEqual(ts1.minimum2.energy, ts2.minimum2.energy)
def write_pathsample_db(db):
writer = WritePathsampleDB(db)
writer.write_db()
