def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system" % nrigid
print "The initial energy is", pot.getEnergy(coords)
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
class TestAAMindist(unittest.TestCase):
def setUp(self):
#GMIN.initialize()
# self.pot = GMINPotential(GMIN)
self.nrigid = 10
self.water = create_water()
self.topology = RBTopology()
self.topology.add_sites([deepcopy(self.water) for i in xrange(self.nrigid)])
# def test_zeroev(self):
# x = self.pot.getCoords()
# zev = self.topology.zeroEV(x)
#
# eps = 1e-5
# for dx in zev:
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
#
# dx = np.random.random(x.shape)
# dx/=np.linalg.norm(dx)
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
def test_distance(self):
for i in xrange(100):
coords1 = np.random.random(6*self.nrigid)*4
coords2 = np.random.random(6*self.nrigid)*4
coords1[:3*self.nrigid]=0
coords2[:3*self.nrigid]=0
measure1 = am.MeasureAngleAxisCluster(self.topology)
measure2 = am.MeasureRigidBodyCluster(self.topology)
#print
self.assertAlmostEqual(measure1.get_dist(coords1, coords2),
measure2.get_dist(coords1, coords2))
def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system"%nrigid
print "The initial energy is", pot.getEnergy(coords)
water = create_base()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.15
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid-1):
self.draw_bonds.append((2*i, 2*i+1))
self.draw_bonds.append((2*i, 2*i+2))
return system
def setUp(self):
#GMIN.initialize()
# self.pot = GMINPotential(GMIN)
self.nrigid = 10
self.water = create_water()
self.topology = RBTopology()
self.topology.add_sites(
[deepcopy(self.water) for i in xrange(self.nrigid)])
def setUp(self):
#GMIN.initialize()
# self.pot = GMINPotential(GMIN)
self.nrigid = 10
self.water = create_water()
self.topology = RBTopology()
self.topology.add_sites([deepcopy(self.water) for i in xrange(self.nrigid)])
def setup_aatopology(self):
self.write_coords_data()
GMIN.initialize()
self.pot = GMINPotential(GMIN)
coords = self.pot.getCoords()
self.nrigid = coords.size / 6
assert (self.nrigid == self.nmol)
#self.nrigid = self.nmol
otp = self.make_otp()
topology = RBTopology()
topology.add_sites([deepcopy(otp) for i in xrange(self.nrigid)])
self.render_scale = 0.2
self.atom_types = topology.get_atomtypes()
self.draw_bonds = []
for i in xrange(self.nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
self.params.double_ended_connect.local_connect_params.tsSearchParams.iprint = 10
return topology
def setup_aatopology(self):
self.write_coords_data()
GMIN.initialize()
self.pot = GMINPotential(GMIN)
coords = self.pot.getCoords()
self.nrigid = coords.size/6
assert(self.nrigid == self.nmol)
#self.nrigid = self.nmol
otp = self.make_otp()
topology = RBTopology()
topology.add_sites([deepcopy(otp) for i in xrange(self.nrigid)])
self.render_scale = 0.2
self.atom_types = topology.get_atomtypes()
self.draw_bonds = []
for i in xrange(self.nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
self.params.double_ended_connect.local_connect_params.tsSearchParams.iprint = 10
return topology
class TestAAMindist(unittest.TestCase):
def setUp(self):
#GMIN.initialize()
# self.pot = GMINPotential(GMIN)
self.nrigid = 10
self.water = create_water()
self.topology = RBTopology()
self.topology.add_sites(
[deepcopy(self.water) for i in xrange(self.nrigid)])
# def test_zeroev(self):
# x = self.pot.getCoords()
# zev = self.topology.zeroEV(x)
#
# eps = 1e-5
# for dx in zev:
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
#
# dx = np.random.random(x.shape)
# dx/=np.linalg.norm(dx)
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
def test_distance(self):
for i in xrange(100):
coords1 = np.random.random(6 * self.nrigid) * 4
coords2 = np.random.random(6 * self.nrigid) * 4
coords1[:3 * self.nrigid] = 0
coords2[:3 * self.nrigid] = 0
measure1 = am.MeasureAngleAxisCluster(self.topology)
measure2 = am.MeasureRigidBodyCluster(self.topology)
#print
self.assertAlmostEqual(measure1.get_dist(coords1, coords2),
measure2.get_dist(coords1, coords2))
