def setUp(self): from pygmin.potentials.rigid_bodies.molecule import Molecule, setupLWOTP from pygmin.potentials.rigid_bodies.sandbox import RBSandbox from pygmin.potentials.lj import LJ from pygmin.optimize import lbfgs_py as quench #set up system nmol = 5 self.nmol = nmol otp = setupLWOTP() #set up a list of molecules mols = [otp for i in range(nmol)] # define the interaction matrix for the system. # for LWOTP there is only one atom type, so this is trivial lj = LJ() interaction_matrix = [[lj]] #set up the RBSandbox object mysys = RBSandbox(mols, interaction_matrix) self.pot = mysys self.nsites = mysys.nsites self.permlist = [range(nmol)] self.coords1 = testmindist.randomCoordsAA(nmol) ret = quench(self.coords1, self.pot.getEnergyGradient) self.coords1 = ret[0]
def testOPT(self): from pygmin.optimize import lbfgs_py as quench coords1 = np.copy(self.coords1) coords1i = np.copy(coords1) coords2 = testmindist.randomCoordsAA(self.nmol) ret = quench(coords2, self.pot.getEnergyGradient) coords2 = ret[0] coords2i = np.copy(coords2) self.runtest(coords1, coords2)
def testOPT(self): from pygmin.optimize import lbfgs_py as quench coords1 = np.copy(self.coords1) coords1i = np.copy(coords1) coords2 = testmindist.randomCoordsAA(self.nmol) ret = quench(coords2, self.pot.getEnergyGradient) coords2 = ret[0] coords2i = np.copy(coords2) self.runtest( coords1, coords2)