def setUp(self):
self.nrigid = 1
self.boxl = np.array([5,5,5])
# self.topology = RBTopologyBulk(self.boxl)
# self.topology.finalize_setup()
# sites = []
# for i in range(self.nrigid):
# sites.append(self.make_molecule())
# self.topology.add_sites(sites)
# self.draw_bonds = []
# for i in xrange(self.nrigid):
# # self.draw_bonds.append((2*i,2*i+1))
# self.draw_bonds.append((3*i, 3*i+1))
# self.draw_bonds.append((3*i, 3*i+2))
# #self.permlist = self.get_permlist()
import pele.angleaxis._otp_bulk as OTP
self.system = OTP.OTPBulk(self.nrigid, self.boxl, 2.5)
self.topology = self.system.aatopology
self.mindist = self.system.get_mindist()
self.transform = TransformPeriodicRigid()
self.measure = MeasurePeriodicRigid(self.topology, self.transform)
self.exact_match = ExactMatchRigidPeriodic(self.measure, accuracy=1e-5)
# self.mindist = MinPermDistBulk(self.boxl, self.measure)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
self.x2same = self.x1.copy()
self.x2trans = self.x1.copy()
trans = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, trans)
def get_mindist(self, **kwargs):
measure = MeasurePeriodicRigid(self.aatopology,
transform=TransformPeriodicRigid())
return MinDistBulkRigid(self.boxvec,
measure,
niter=10,
transform=TransformPeriodicRigid(),
verbose=False,
tol=0.01,
accuracy=0.01)
