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)