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 = 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 getEnergy(self, coords):
E = GMINPotential.getEnergy(self, coords)
ca = CoordsAdapter(nrigid=coords.size / 6, coords=coords)
RMX = [rmdrvt(p, True) for p in ca.rotRigid]
xback = np.array([x - 0.4 * np.dot(r[0], np.array([1.0, 0.0, 0.0])) for x, r in zip(ca.posRigid, RMX)])
xbase = np.array([x + 0.4 * np.dot(r[0], np.array([1.0, 0.0, 0.0])) for x, r in zip(ca.posRigid, RMX)])
Eangle = 0
v2 = xback[1] - xback[0]
v2 /= np.linalg.norm(v2)
for i in xrange(1, ca.nrigid - 1):
v1 = -v2.copy()
v2 = xback[i + 1] - xback[i]
v2 /= np.linalg.norm(v2)
theta = np.arccos(np.dot(v1, v2))
Eangle += 0.5 * self.k * (theta - self.theta0) ** 2
# add the torsion angle
Etorsion = 0
if self.use_torsion:
for i in xrange(ca.nrigid - 3):
theta = dihedral_angle(xback[i : i + 4])
Etorsion += U_torsion_back(theta)
return E + Eangle + Etorsion
def getEnergy(self, coords):
E = GMINPotential.getEnergy(self, coords)
ca = CoordsAdapter(nrigid=old_div(coords.size, 6), coords=coords)
RMX = [rotMatDeriv(p, True) for p in ca.rotRigid]
xback = np.array([
x - 0.4 * np.dot(r[0], np.array([1., 0., 0.]))
for x, r in zip(ca.posRigid, RMX)
])
xbase = np.array([
x + 0.4 * np.dot(r[0], np.array([1., 0., 0.]))
for x, r in zip(ca.posRigid, RMX)
])
Eangle = 0
v2 = xback[1] - xback[0]
v2 /= np.linalg.norm(v2)
for i in range(1, ca.nrigid - 1):
v1 = -v2.copy()
v2 = xback[i + 1] - xback[i]
v2 /= np.linalg.norm(v2)
theta = np.arccos(np.dot(v1, v2))
Eangle += 0.5 * self.k * (theta - self.theta0)**2
# add the torsion angle
Etorsion = 0
if self.use_torsion:
for i in range(ca.nrigid - 3):
theta = dihedral_angle(xback[i:i + 4])
Etorsion += U_torsion_back(theta)
return E + Eangle + Etorsion
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
# define the whole water system
system = RBSystem()
system.add_sites([deepcopy(water) for i in range(nrigid)])
# this is an easy access wrapper for coordinates array
ca = system.coords_adapter(coords)
#buildingblocks.rotate(3.0, ca.rotRigid[-1:])
#ret = mylbfgs(coords, pot.getEnergyGradient, iprint=0)
#coords2 = ret[0]
#np.savetxt("coords1_2.txt", coords1)
#np.savetxt("coords2_2.txt", coords2)
coords1 = np.loadtxt("coords1.txt")
coords2 = np.loadtxt("coords2.txt")
print(pot.getEnergy(coords1), pot.getEnergy(coords2))
NEBquenchParams = dict()
NEBquenchParams["nsteps"] = 200
NEBquenchParams["iprint"] = 1
NEBquenchParams["maxstep"] = 0.1
NEBquenchParams["maxErise"] = 0.1
NEBquenchParams["tol"] = 1e-6
NEBquenchRoutine = mylbfgs
decp = dict()
decp["local_connect_params"] = dict()
decp["local_connect_params"]["NEBparams"] = dict()
decp["local_connect_params"]["NEBparams"]["NEBquenchParams"] = NEBquenchParams
decp["local_connect_params"]["NEBparams"][
"NEBquenchRoutine"] = NEBquenchRoutine
# define the whole water system
system = RBSystem()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
# this is an easy access wrapper for coordinates array
ca = system.coords_adapter(coords)
#buildingblocks.rotate(3.0, ca.rotRigid[-1:])
#ret = mylbfgs(coords, pot.getEnergyGradient, iprint=0)
#coords2 = ret[0]
#np.savetxt("coords1_2.txt", coords1)
#np.savetxt("coords2_2.txt", coords2)
coords1 = np.loadtxt("coords1.txt")
coords2 = np.loadtxt("coords2.txt")
print pot.getEnergy(coords1), pot.getEnergy(coords2)
NEBquenchParams = dict()
NEBquenchParams["nsteps"] = 200
NEBquenchParams["iprint"] = 1
NEBquenchParams["maxstep"] = 0.1
NEBquenchParams["maxErise"] = 0.1
NEBquenchParams["tol"] = 1e-6
NEBquenchRoutine = mylbfgs
decp = dict()
decp["local_connect_params"] = dict()
decp["local_connect_params"]["NEBparams"] = dict()
decp["local_connect_params"]["NEBparams"]["NEBquenchParams"] = NEBquenchParams
decp["local_connect_params"]["NEBparams"]["NEBquenchRoutine"] = NEBquenchRoutine
k = 10.