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 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)
