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 test_LWOTP(nmol=5):
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
printlist = []
#set up system
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)
nsites = mysys.nsites
permlist = [range(nmol)]
#define initial coords
coords1 = randomCoords(nmol)
printlist.append((coords1.copy(), "very first"))
#quench X1
ret = quench(coords1, mysys.getEnergyGradient)
coords1 = ret[0]
#define initial coords2
coords2 = randomCoords(nmol)
printlist.append((coords2.copy(), "very first"))
#quench X2
ret = quench(coords2, mysys.getEnergyGradient)
coords2 = ret[0]
coords2in = coords2.copy()
printlist.append((coords1.copy(), "after quench"))
printlist.append((coords2.copy(), "after quench"))
print "******************************"
print "testing for OTP not isomer"
print "******************************"
d, c1new, c2new = test(coords1, coords2, mysys, permlist)
print "******************************"
print "testing for OTP ISOMER"
print "******************************"
coords1 = coords2in.copy()
coords2 = c2new.copy()
#try to reverse the permutations and symmetry operations we just applied
test(coords1, coords2, mysys, permlist)
def test_LWOTP(nmol = 5):
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
printlist = []
#set up system
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)
nsites = mysys.nsites
permlist = [range(nmol)]
#define initial coords
coords1 = randomCoords(nmol)
printlist.append( (coords1.copy(), "very first"))
#quench X1
ret = quench( coords1, mysys.getEnergyGradient)
coords1 = ret[0]
#define initial coords2
coords2 = randomCoords(nmol)
printlist.append( (coords2.copy(), "very first"))
#quench X2
ret = quench( coords2, mysys.getEnergyGradient)
coords2 = ret[0]
coords2in = coords2.copy()
printlist.append((coords1.copy(), "after quench"))
printlist.append((coords2.copy(), "after quench"))
print "******************************"
print "testing for OTP not isomer"
print "******************************"
d, c1new, c2new = test(coords1, coords2, mysys, permlist)
print "******************************"
print "testing for OTP ISOMER"
print "******************************"
coords1 = coords2in.copy()
coords2 = c2new.copy()
#try to reverse the permutations and symmetry operations we just applied
test(coords1, coords2, mysys, permlist)
def createSystem(self):
import pygmin.potentials.lj as lj
from pygmin.potentials.rigid_bodies.molecule import setupLWOTP
from pygmin.potentials.rigid_bodies.sandbox import RBSandbox
#setup otp molecule
otp = setupLWOTP()
#set up interactions between sites
potential = lj.LJ()
interaction_matrix = [[potential]]
#set up system
mols = [otp for i in range(self.nmol)]
mysys = RBSandbox(mols, interaction_matrix)
return mysys
