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_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
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):
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_aatopology(self):
"""this sets up the topology for the whole rigid body system"""
topology = RBTopology()
topology.add_sites([self.make_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))
return topology
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_aatopology(self):
"""this sets up the topology for the whole rigid body system"""
topology = RBTopology()
topology.add_sites([make_triangular_plate() 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))
topology.finalize_setup()
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
