def nebtest(MyNEB=NEB, nimages=22):
import pylab as pl
from interpolate import InterpolatedPath
from pygmin import defaults
from pygmin.optimize import lbfgs_py
defaults.NEBquenchRoutine = lbfgs_py
defaults.NEBquenchParams["iprint"]=1
defaults.NEBquenchParams["debug"]=True
defaults.NEBquenchParams["maxErise"]=0.1
x = np.arange(.5, 5., .05)
y = np.arange(.5, 5., .05)
z = np.zeros([len(x), len(y)])
potential = test.leps()
for i in range(0, len(x)):
for j in range(0, len(y)):
z[j, i] = potential.getEnergy([x[i], y[j]])
print "done"
#z[z>0.] = 0.
#pl.imshow(z)
#pl.show()
initial = np.array([.75, 2.]) #np.random.random(3)
final = np.array([2., .75]) #np.random.random(3)
# from pygmin.optimize import quench
# print "quench initial"
# ret = quench.lbfgs_py(initial, potential.getEnergyGradient)
# initial = ret[0]
# print "quench final"
# ret = quench.quench(final, potential.getEnergyGradient)
# final = ret[0]
# print "done with quenching"
# print initial, final
#print "Initial: ", initial
#print "Final: ", final
#pl.imshow(z)
neb = MyNEB(InterpolatedPath(initial, final, nimages) ,potential, k=1000, dneb=False)
tmp = neb.coords
energies_interpolate = neb.energies.copy()
pl.figure()
pl.subplot(2,2,1)
pl.subplots_adjust(wspace=0.3, left=0.05, right=0.95, bottom = 0.14)
pl.title("path")
#pl.contourf(x, y, z)
pl.pcolor(x, y, z, vmax=-0.5, cmap=pl.cm.PuBu)
pl.colorbar()
pl.plot(tmp[:, 0], tmp[:, 1], 'ko-')
print "optimizing NEB"
neb.optimize()#quenchRoutine=quench.fire)
print "done"
tmp = neb.coords
pl.plot(tmp[:, 0], tmp[:, 1], 'ro-')
pl.xlabel("x")
pl.ylabel("y")
pl.axis(xmin=0.5, xmax=2.5, ymin=0.5, ymax=2.5)
pl.subplot(1,2,2)
pl.title("energy")
pl.plot(energies_interpolate, 'ko-', label="interpolate")
pl.plot(neb.energies, 'ro-', label="neb")
pl.xlabel("image")
pl.ylabel("energy")
pl.legend(loc='best')
pl.subplot(1,2,2)
pl.title("energy")
pl.plot(energies_interpolate, 'ko-', label="interpolate")
pl.plot(neb.energies, 'ro-', label="neb")
pl.xlabel("image")
pl.ylabel("energy")
pl.legend(loc='best')
pl.show()
self.potential = potential
self.trajectory=[]
def getEnergyGradient(self, x):
self.trajectory.append(x)
return self.potential.getEnergyGradient(x)
def getEnergy(self, x):
return self.potential.getEnergy(x)
if __name__ == "__main__":
import pylab as pl
x = np.arange(.5, 5., .05)
y = np.arange(.5, 5., .05)
z = np.zeros([len(x), len(y)])
potential = potwrap(test.leps())
for i in range(0, len(x)):
for j in range(0, len(y)):
z[j, i] = potential.getEnergy([x[i], y[j]])
x0 = np.array([.75, 1.5]) #np.random.random(3)
#final = np.array([2., .75]) #np.random.random(3)
pl.pcolor(x, y, z, vmax=-0.5, cmap=pl.cm.PuBu)
tau=np.array([0.5,-1.])#np.random.random(2)-0.5
x1 = x0 + 0.1*tau
pl.plot([x0[0], x1[0]], [x0[1], x1[1]])
ret = findTransitionState_dimer(x0, potential, tau)
x0 = ret.coords
tau=ret.eigenvec
E = ret.energy
x1 = x0 + 0.1*tau
def nebtest(MyNEB=NEB, nimages=22):
import pylab as pl
from interpolate import InterpolatedPath
from pygmin.optimize import lbfgs_py
NEBquenchParams = dict()
NEBquenchParams["iprint"] = 20
NEBquenchParams["debug"] = True
NEBquenchParams["maxErise"] = 0.1
x = np.arange(.5, 5., .05)
y = np.arange(.5, 5., .05)
z = np.zeros([len(x), len(y)])
potential = test.leps()
for i in range(0, len(x)):
for j in range(0, len(y)):
z[j, i] = potential.getEnergy([x[i], y[j]])
print "done"
#z[z>0.] = 0.
#pl.imshow(z)
#pl.show()
initial = np.array([.75, 2.]) #np.random.random(3)
final = np.array([2., .75]) #np.random.random(3)
# from pygmin.optimize import quench
# print "quench initial"
# ret = quench.lbfgs_py(initial, potential.getEnergyGradient)
# initial = ret[0]
# print "quench final"
# ret = quench.quench(final, potential.getEnergyGradient)
# final = ret[0]
# print "done with quenching"
# print initial, final
#print "Initial: ", initial
#print "Final: ", final
#pl.imshow(z)
neb = MyNEB(InterpolatedPath(initial, final, nimages),
potential,
k=1000,
dneb=False,
quenchParams=NEBquenchParams)
tmp = neb.coords
energies_interpolate = neb.energies.copy()
pl.figure()
pl.subplot(2, 2, 1)
pl.subplots_adjust(wspace=0.3, left=0.05, right=0.95, bottom=0.14)
pl.title("path")
#pl.contourf(x, y, z)
pl.pcolor(x, y, z, vmax=-0.5, cmap=pl.cm.PuBu)
pl.colorbar()
pl.plot(tmp[:, 0], tmp[:, 1], 'ko-')
print "optimizing NEB"
neb.optimize() #quenchRoutine=quench.fire)
print "done"
tmp = neb.coords
pl.plot(tmp[:, 0], tmp[:, 1], 'ro-')
pl.xlabel("x")
pl.ylabel("y")
pl.axis(xmin=0.5, xmax=2.5, ymin=0.5, ymax=2.5)
pl.subplot(1, 2, 2)
pl.title("energy")
pl.plot(energies_interpolate, 'ko-', label="interpolate")
pl.plot(neb.energies, 'ro-', label="neb")
pl.xlabel("image")
pl.ylabel("energy")
pl.legend(loc='best')
pl.subplot(1, 2, 2)
pl.title("energy")
pl.plot(energies_interpolate, 'ko-', label="interpolate")
pl.plot(neb.energies, 'ro-', label="neb")
pl.xlabel("image")
pl.ylabel("energy")
pl.legend(loc='best')
pl.show()
