def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d PAP molecules in the system" % nrigid
print "The initial energy is", pot.getEnergy(coords)
water = create_pap()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.1
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
def setup_aatopology(self):
GMIN.initialize()
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = old_div(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 range(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.15
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in range(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):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites(
[create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
def setup_aatopology(self):
water_sites, ref = water(self.xyzfile)
rbsystem = RBTopology()
rbsystem.add_sites(water_sites)
rbsystem.finalize_setup()
#print len(rbsystem.sites), len(rbsystem.indices)
print "I have %d water molecules in the system" % len(rbsystem.sites)
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites)*6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.atom_indices[0]] - site.atom_positions[0]
pot = LJ(eps=0.1550, sig=3.1536)
# get the flattened coordinate array
print "The initial energy is", pot.getEnergy(ref.coords.flatten())
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print "rbpot.getEnergy(rbcoords.coords)", rbpot.getEnergy(rbcoords.coords)
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g-g_n)
# coords = rbpot.getCoords()
# nrigid = rbcoords.size / 6
# print "nrigid", nrigid
self.potential = rbpot
self.nrigid = len(rbsystem.sites)
self.render_scale = 0.3
self.atom_types = rbsystem.get_atomtypes()
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 _ in xrange(self.nrigid)])
self.topology.finalize_setup()
def make_atom_indices_cpp_topology(self, atom_indices=None):
sites = [make_otp() for _ in xrange(self.nrigid)]
if atom_indices is None:
atom_indices = np.array(range(self.nrigid * 3), dtype=int)
np.random.shuffle(atom_indices)
i = 0
for site in sites:
site.atom_indices = atom_indices[i:i + site.get_natoms()].copy()
i += site.get_natoms()
topology = RBTopology()
topology.add_sites(sites)
topology.finalize_setup(use_cpp=False)
return topology, atom_indices
def setUp(self):
nrigid = 3
self.topology = RBTopology()
self.topology.add_sites([make_otp() for i in range(nrigid)])
self.topology.finalize_setup()
cartesian_potential = LJ()
self.pot = RBPotentialWrapper(self.topology, cartesian_potential)
self.x0 = _x03
self.x0 = np.array(self.x0)
self.e0 = -17.3387670023
assert nrigid * 6 == self.x0.size
self.x0atomistic = _x03_atomistic
self.nrigid = nrigid
def setup_aatopology(self):
"""this sets up the topology for the whole rigid body system"""
topology = RBTopology()
topology.add_sites([self.make_otp() for _ 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))
topology.finalize_setup()
return topology
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)
def make_normal_cpp_topology(self):
sites = [make_otp() for _ in xrange(self.nrigid)]
normal_topology = RBTopology()
normal_topology.add_sites(sites)
normal_topology.finalize_setup()
return normal_topology