def Align(self, coords1, coords2):
from pygmin.mindist import rmsfit,aamindist
potential = GMINPotential(GMIN)
ca1 = CoordsAdapter(nrigid=coords1.size/6, coords = coords1)
ca2 = CoordsAdapter(nrigid=coords2.size/6, coords = coords2)
rot = rmsfit.findrotation_kabsch(ca2.posRigid, ca1.posRigid)
ca2.posRigid[:] = np.dot(rot,ca2.posRigid.transpose()).transpose()
for p in ca2.rotRigid:
p[:] = rotations.mx2aa((np.dot(rot, rotations.aa2mx(p))))
print "before"
print potential.getEnergy(coords1), potential.getEnergy(coords2)
print ca2.rotRigid - ca1.rotRigid
for p1,p2 in zip(ca1.rotRigid, ca2.rotRigid):
p1[:],p2[:] = aamindist.aadistance(p1, p2)
print "after"
print potential.getEnergy(coords1), potential.getEnergy(coords2)
print ca2.rotRigid - ca1.rotRigid
path = InterpolatedPath(coords1, coords2, 40)
print potential.getEnergy(path[0])
print "Interpolated energies"
for x in InterpolatedPath(coords1, coords2, 40):
print potential.getEnergy(x)
print "done"
return 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 = 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 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 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.])) 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 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=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.]))
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 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
traj = open("traj.xyz", "w")
#for x in path:
# #export_xyz(traj, x)
# #ret = quench.mylbfgs(x, pot.getEnergyGradient)
# #print i,pot.getEnergy(x), ret[1]
#
# # export_xyz(traj, ret[0])
db=Database(db="oxdna.sqlite")
path[0]=db.minima()[19].coords
path[-1]=db.minima()[0].coords
e1 = []
e2 = []
e1.append(pot.getEnergy(path[0]))
e2.append(pot.getEnergy(path[0]))
for i in xrange(1):
for i in xrange(len(path)-1):
e1.append(pot.getEnergy(path[i+1]))
c1 = CoordsAdapter(nrigid=13, coords = path[i])
c2 = CoordsAdapter(nrigid=13, coords = path[i+1])
com1 = np.sum(c1.posRigid,axis=0) / float(13)
com2 = np.sum(c1.posRigid,axis=0) / float(13)
c1.posRigid-=com1
c2.posRigid-=com2
mx = findrotation_kabsch(c2.posRigid, c1.posRigid)
#print mx
c2.posRigid[:] = np.dot(mx, c2.posRigid.transpose()).transpose()
for p in c2.rotRigid:
# 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)
defaults.NEBquenchParams["nsteps"] = 200
defaults.NEBquenchParams["iprint"] = 1
defaults.NEBquenchParams["maxstep"] = 0.1
defaults.NEBquenchParams["maxErise"] = 0.1
defaults.NEBquenchParams["tol"] = 1e-6
defaults.NEBquenchRoutine = mylbfgs
k = 10.
nimages=50
dneb=True
#print coords2[-6:],coords1[-6:]
path = tip4p.get_path(system, coords1, coords2, nimages)
path_energy = [pot.getEnergy(coords) for coords in path]
# 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
