def findTransitionState_dimer(x0, potential, direction=None, tol=1.0e-6, maxstep=0.1, iprint=-1, **kwargs):
'''
Wrapper for DimerSearch to find transition states
'''
search = DimerSearch(x0, potential, direction=direction, **kwargs)
#search.findNextTS(direction)
#search.findNextTS(direction)
#search.findNextTS(direction)
x, E, rms, tmp = fire(x0, search.getEnergyGradient, tol=tol, maxstep=maxstep, iprint=iprint)
#x, E, rms, tmp = quench.mylbfgs(x0, search.getEnergyGradient, tol=tol, maxstep=maxstep, maxErise=1000.)
from collections import namedtuple
return namedtuple("TransitionStateResults", "coords,energy,eigenval,eigenvec,rms")(x, E, 0.0, search.tau, rms)
def _uphill_search(x0, search, push, push_minrms):
ev = search.tau
evecs = search.get_eigenvecs(x0)
#print len(evecs)
x1 = x0.copy()
while True:
x1+=push*ev
g = search.getOrthogonalGradient(x1, evecs)
#print np.linalg.norm(g)
rms = np.linalg.norm(g)/np.sqrt(len(g))
#print "rms",rms
if (rms > push_minrms):
# print "rms final",rms
break
#x1 = x0 + np.random.random(x0.shape)*0.1
#search.tau_done=[]
#search.x0 = x1
#search.findNextTS()
return fire(x1, search.getEnergyGradient, tol=1e-6)
def _uphill_search(x0, search, push, push_minrms):
ev = search.tau
evecs = search.get_eigenvecs(x0)
# print len(evecs)
x1 = x0.copy()
while True:
x1 += push * ev
g = search.getOrthogonalGradient(x1, evecs)
# print np.linalg.norm(g)
rms = old_div(np.linalg.norm(g), np.sqrt(len(g)))
# print "rms",rms
if rms > push_minrms:
# print "rms final",rms
break
# x1 = x0 + np.random.random(x0.shape)*0.1
# search.tau_done=[]
# search.x0 = x1
# search.findNextTS()
return fire(x1, search.getEnergyGradient, tol=1e-6)
print(eo) # energy
print(go[0:5])
print("\n-----------------")
print("quench\n")
# lbfgs
# ret = quench( coordsVec, pot.getEnergyGradient, iprint=-1 , tol = 1e-3, nsteps=100)
# core dump!
# cg
# ret = cg( coordsVec, pot.getEnergyGradient)
# runtime error -- ValueError: The truth value of an array with more than ...
# fire
retOpmm = fire(coordsVec, pot, tol=1e-3, nsteps=1000)
# works but quenched energy is higher!
print("quenched energy ", retOpmm.energy)
print("rms gradient", retOpmm.rms)
print("number of function calls", retOpmm.nfev)
# -------- GMIN
print("\n\nCompare with GMIN")
GMIN.initialize() # reads coords.inpcrd and coords.prmtop
pot = gminpot.GMINPotential(GMIN)
coords = pot.getCoords()
enerGmin = pot.getEnergy(coords)
egmin, gminEGrad = pot.getEnergyGradient(coords)
print eo # energy
print go[0:5]
print "\n-----------------"
print "quench\n"
# lbfgs
# ret = quench( coordsVec, pot.getEnergyGradient, iprint=-1 , tol = 1e-3, nsteps=100)
# core dump!
# cg
# ret = cg( coordsVec, pot.getEnergyGradient)
# runtime error -- ValueError: The truth value of an array with more than ...
# fire
retOpmm = fire( coordsVec, pot, tol = 1e-3, nsteps=1000)
# works but quenched energy is higher!
print "quenched energy ", retOpmm.energy
print "rms gradient", retOpmm.rms
print "number of function calls", retOpmm.nfev
# -------- GMIN
print "\n\nCompare with GMIN"
GMIN.initialize() # reads coords.inpcrd and coords.prmtop
pot = gminpot.GMINPotential(GMIN)
coords = pot.getCoords()
enerGmin = pot.getEnergy(coords)
egmin,gminEGrad = pot.getEnergyGradient(coords)