def get_compare_exact(self, **kwargs):
if self.pot.periodic:
permlist = self.get_permlist()
boxlengths = np.ones(3) * self.pot.boxl
measure = MeasurePeriodic(boxlengths, permlist)
return ExactMatchPeriodic(measure, accuracy=.1)
else:
return BLJCluster.get_compare_exact(self, **kwargs)
def get_compare_exact(self, **kwargs):
if self.pot.periodic:
permlist = self.get_permlist()
boxlengths = np.ones(3) * self.pot.boxl
measure = MeasurePeriodic(boxlengths, permlist)
return ExactMatchPeriodic(measure, accuracy=.1)
else:
return BLJCluster.get_compare_exact(self, **kwargs)
class TestBLJClusterSystem(unittest.TestCase):
def setUp(self):
self.natoms = 13
self.ntypeA = 8
self.system = BLJCluster(self.natoms, self.ntypeA)
def test_database_property(self):
db = self.system.create_database()
p = db.get_property("natoms")
self.assertIsNotNone(p)
self.assertEqual(p.value(), self.natoms)
p = db.get_property("ntypeA")
self.assertIsNotNone(p)
self.assertEqual(p.value(), self.ntypeA)
class TestBLJClusterSystem(unittest.TestCase):
def setUp(self):
self.natoms = 13
self.ntypeA = 8
self.system = BLJCluster(self.natoms, self.ntypeA)
def test_database_property(self):
db = self.system.create_database()
p = db.get_property("natoms")
self.assertIsNotNone(p)
self.assertEqual(p.value(), self.natoms)
p = db.get_property("ntypeA")
self.assertIsNotNone(p)
self.assertEqual(p.value(), self.ntypeA)
def setUp(self):
self.natoms = 13
self.ntypeA = 8
self.system = BLJCluster(self.natoms, self.ntypeA)
def draw(self, coordslinear, index):
from pele.systems._opengl_tools import draw_box
put_in_box(coordslinear, self.boxvec)
BLJCluster.draw(self, coordslinear, index, subtract_com=False)
draw_box(self.boxvec)
# only testing below here
#
def start():
wnd.start()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pele.systems import LJCluster, BLJCluster
pl.ion()
natoms = 13
system = BLJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms,)
db = system.create_database()#dbname)
#get some minima
if True:
bh = system.get_basinhopping(database=db)
bh.run(20)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]
def setUp(self):
self.natoms = 13
self.ntypeA = 8
self.system = BLJCluster(self.natoms, self.ntypeA)
def on_buttonBox_accepted(self):
self.get_input()
self.close()
def on_buttonBox_rejected(self):
self.close()
if __name__ == "__main__":
# create a pop up window to get the number of atoms
app = QtGui.QApplication(sys.argv)
dialog = BLJDialog()
dialog.exec_()
if dialog.natoms is None:
sys.exit()
print(dialog.ntypeA, "A atoms interacting with eps", dialog.epsAA, "sig", dialog.sigAA)
print(dialog.natoms - dialog.ntypeA, "B atoms interacting with eps", dialog.epsBB, "sig", dialog.sigBB)
print("The A and B atoms interact with eps", dialog.epsAB, "sig", dialog.sigAB)
# create the system and start the gui
# (note: since the application is already started we need to pass it to run_gui)
system = BLJCluster(dialog.natoms, dialog.ntypeA,
sigAB=dialog.sigAB,
epsAB=dialog.epsAB,
sigBB=dialog.sigBB,
epsBB=dialog.epsBB,
)
run_gui(system, application=app)
# only testing below here
#
def start():
wnd.start()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pele.systems import LJCluster, BLJCluster
pl.ion()
natoms = 13
system = BLJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms,)
db = system.create_database()#dbname)
#get some minima
if True:
bh = system.get_basinhopping(database=db)
bh.run(20)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]
def draw(self, coordslinear, index):
from pele.systems._opengl_tools import draw_box
put_in_box(coordslinear, self.boxvec)
BLJCluster.draw(self, coordslinear, index, subtract_com=False)
draw_box(self.boxvec)
