def guessts(coords1, coords2, pot):
from pele.optimize import lbfgs_py as quench
# from pele.mindist.minpermdist_stochastic import minPermDistStochastic as mindist
from pele.transition_states import NEB
from pele.systems import LJCluster
ret1 = quench(coords1, pot.getEnergyGradient)
ret2 = quench(coords2, pot.getEnergyGradient)
coords1 = ret1[0]
coords2 = ret2[0]
natoms = len(coords1)/3
system = LJCluster(natoms)
mindist = system.get_mindist()
dist, coords1, coords2 = mindist(coords1, coords2)
print "dist", dist
print "energy coords1", pot.getEnergy(coords1)
print "energy coords2", pot.getEnergy(coords2)
from pele.transition_states import InterpolatedPath
neb = NEB(InterpolatedPath(coords1, coords2, 20), pot)
#neb.optimize(quenchParams={"iprint" : 1})
neb.optimize(iprint=-30, nsteps=100)
neb.MakeAllMaximaClimbing()
#neb.optimize(quenchParams={"iprint": 30, "nsteps":100})
for i in xrange(len(neb.energies)):
if(neb.isclimbing[i]):
coords = neb.coords[i,:]
return pot, coords, neb.coords[0,:], neb.coords[-1,:]
def guesstsATLJ():
from pele.potentials.ATLJ import ATLJ
pot = ATLJ(Z = 2.)
a = 1.12 #2.**(1./6.)
theta = 60./360*np.pi
coords1 = np.array([ 0., 0., 0., \
-a, 0., 0., \
-a/2, -a*np.cos(theta), 0. ])
coords2 = np.array([ 0., 0., 0., \
-a, 0., 0., \
a, 0., 0. ])
from pele.optimize import lbfgs_py as quench
from pele.transition_states import InterpolatedPath
ret1 = quench(coords1, pot.getEnergyGradient)
ret2 = quench(coords2, pot.getEnergyGradient)
coords1 = ret1[0]
coords2 = ret2[0]
from pele.transition_states import NEB
neb = NEB(InterpolatedPath(coords1, coords2, 30), pot)
neb.optimize()
neb.MakeAllMaximaClimbing()
#neb.optimize()
for i in xrange(len(neb.energies)):
if(neb.isclimbing[i]):
coords = neb.coords[i,:]
return pot, coords
def test_LWOTP(nmol=5):
from pele.potentials.rigid_bodies.molecule import Molecule, setupLWOTP
from pele.potentials.rigid_bodies.sandbox import RBSandbox
from pele.potentials.lj import LJ
from pele.optimize import lbfgs_py as quench
printlist = []
# set up system
otp = setupLWOTP()
# set up a list of molecules
mols = [otp for i in range(nmol)]
# define the interaction matrix for the system.
# for LWOTP there is only one atom type, so this is trivial
lj = LJ()
interaction_matrix = [[lj]]
# set up the RBSandbox object
mysys = RBSandbox(mols, interaction_matrix)
nsites = mysys.nsites
permlist = [range(nmol)]
# define initial coords
coords1 = randomCoords(nmol)
printlist.append((coords1.copy(), "very first"))
# quench X1
ret = quench(coords1, mysys.getEnergyGradient)
coords1 = ret[0]
# define initial coords2
coords2 = randomCoords(nmol)
printlist.append((coords2.copy(), "very first"))
# quench X2
ret = quench(coords2, mysys.getEnergyGradient)
coords2 = ret[0]
coords2in = coords2.copy()
printlist.append((coords1.copy(), "after quench"))
printlist.append((coords2.copy(), "after quench"))
print "******************************"
print "testing for OTP not isomer"
print "******************************"
d, c1new, c2new = test(coords1, coords2, mysys, permlist)
print "******************************"
print "testing for OTP ISOMER"
print "******************************"
coords1 = coords2in.copy()
coords2 = c2new.copy()
# try to reverse the permutations and symmetry operations we just applied
test(coords1, coords2, mysys, permlist)
def main(): # pragma: no cover
#test class
natoms = 12
coords = np.random.uniform(-1,1,natoms*3)*2
lj = LJ()
E = lj.getEnergy(coords)
print "E", E
E, V = lj.getEnergyGradient(coords)
print "E", E
print "V"
print V
print "try a quench"
from pele.optimize import mylbfgs as quench
quench( coords, lj, iprint=1 )
def setUp(self):
from pele.potentials.rigid_bodies.molecule import Molecule, setupLWOTP
from pele.potentials.rigid_bodies.sandbox import RBSandbox
from pele.potentials.lj import LJ
from pele.optimize import lbfgs_py as quench
# set up system
nmol = 5
self.nmol = nmol
otp = setupLWOTP()
# set up a list of molecules
mols = [otp for i in range(nmol)]
# define the interaction matrix for the system.
# for LWOTP there is only one atom type, so this is trivial
lj = LJ()
interaction_matrix = [[lj]]
# set up the RBSandbox object
mysys = RBSandbox(mols, interaction_matrix)
self.pot = mysys
self.nsites = mysys.nsites
self.permlist = [range(nmol)]
self.coords1 = testmindist.randomCoordsAA(nmol)
ret = quench(self.coords1, self.pot.getEnergyGradient)
self.coords1 = ret[0]
def runtest(X, pot, natoms = 100, iprint=-1):
from _lbfgs_py import PrintEvent
tol = 1e-5
maxstep = 0.005
Xinit = np.copy(X)
e, g = pot.getEnergyGradient(X)
print "energy", e
lbfgs = LBFGS(X, pot, maxstep = 0.1, nsteps=10000, tol=tol,
iprint=iprint, H0=2.)
printevent = PrintEvent( "debugout.xyz")
lbfgs.attachEvent(printevent)
ret = lbfgs.run()
print ret
print ""
print "now do the same with scipy lbfgs"
from pele.optimize import lbfgs_scipy as quench
ret = quench(Xinit, pot, tol = tol)
print ret
#print ret[1], ret[2], ret[3]
if False:
print "now do the same with scipy bfgs"
from pele.optimize import bfgs as oldbfgs
ret = oldbfgs(Xinit, pot, tol = tol)
print ret
if False:
print "now do the same with gradient + linesearch"
import _bfgs
gpl = _bfgs.GradientPlusLinesearch(Xinit, pot, maxstep = 0.1)
ret = gpl.run(1000, tol = 1e-6)
print ret
if False:
print "calling from wrapper function"
from pele.optimize import lbfgs_py
ret = lbfgs_py(Xinit, pot, tol = tol)
print ret
if True:
print ""
print "now do the same with lbfgs_py"
from pele.optimize import lbfgs_py
ret = lbfgs_py(Xinit, pot, tol = tol)
print ret
try:
import pele.utils.pymolwrapper as pym
pym.start()
for n, coords in enumerate(printevent.coordslist):
coords=coords.reshape(natoms, 3)
pym.draw_spheres(coords, "A", n)
except ImportError:
print "error loading pymol"
def main(): # pragma: no cover
# test class
natoms = 12
coords = np.random.uniform(-1, 1, natoms * 3) * 2
lj = LJ()
E = lj.getEnergy(coords)
print("E", E)
E, V = lj.getEnergyGradient(coords)
print("E", E)
print("V")
print(V)
print("try a quench")
from pele.optimize import mylbfgs as quench
quench(coords, lj, iprint=1)
def get_minimizer(self, nsteps=1e6, M=4, iprint=0, maxstep=1.0, **kwargs):
from pele.optimize import lbfgs_cpp as quench
return lambda coords: quench(coords,
self.get_potential(),
tol=self.minimizer_tolerance,
nsteps=nsteps,
M=M,
iprint=iprint,
maxstep=maxstep,
**kwargs)
def main():
#test class
natoms = 3
coords = np.random.uniform(-1,1,natoms*3)*2
lj = ATLJ(Z=1.)
E = lj.getEnergy(coords)
print "E", E
E, V = lj.getEnergyGradient(coords)
print "E", E
print "V"
print V
print "try a quench"
from pele.optimize import mylbfgs as quench
ret = quench( coords, lj, iprint=-1 )
#quench( coords, lj.getEnergyGradientNumerical, iprint=1 )
print "energy ", ret.energy
print "rms gradient", ret.rms
print "number of function calls", ret.nfev
from pele.utils.xyz import write_xyz
coords = ret.coords
printlist = []
for i in range(100):
coords = np.random.uniform(-1,1,natoms*3)*2
#coords = np.array([0,0,1., 0,0,0, 0,0,2])
#coords[6:] += np.random.uniform(-1,1,3)*0.1
ret = quench( coords, lj.getEnergyGradient, iprint=-1 )
coords = ret.coords
X = np.reshape(coords, [natoms,3])
com = X.sum(0) / natoms
X[:,:] -= com[np.newaxis,:]
printlist.append(np.reshape(X, natoms*3))
with open("out.xyz", "w") as fout:
for coords in printlist:
write_xyz(fout, coords)
def testOPT(self):
from pele.optimize import lbfgs_py as quench
coords1 = np.copy(self.coords1)
coords1i = np.copy(coords1)
coords2 = testmindist.randomCoordsAA(self.nmol)
ret = quench(coords2, self.pot.getEnergyGradient)
coords2 = ret[0]
coords2i = np.copy(coords2)
self.runtest(coords1, coords2)
def testing(): # pragma: no cover
# test class
natoms = 3
coords = np.random.uniform(-1, 1, natoms * 3) * 2
lj = ATLJ(Z=1.)
E = lj.getEnergy(coords)
print("E", E)
E, V = lj.getEnergyGradient(coords)
print("E", E)
print("V")
print(V)
print("try a quench")
from pele.optimize import mylbfgs as quench
ret = quench(coords, lj, iprint=-1)
print("energy ", ret.energy)
print("rms gradient", ret.rms)
print("number of function calls", ret.nfev)
from pele.utils.xyz import write_xyz
printlist = []
for i in range(100):
coords = np.random.uniform(-1, 1, natoms * 3) * 2
ret = quench(coords, lj.getEnergyGradient, iprint=-1)
coords = ret.coords
X = np.reshape(coords, [natoms, 3])
com = X.sum(0) / natoms
X[:, :] -= com[np.newaxis, :]
printlist.append(np.reshape(X, natoms * 3))
with open("out.xyz", "w") as fout:
for coords in printlist:
write_xyz(fout, coords)
def testing(): # pragma: no cover
# test class
natoms = 3
coords = np.random.uniform(-1, 1, natoms * 3) * 2
lj = ATLJ(Z=1.)
E = lj.getEnergy(coords)
print("E", E)
E, V = lj.getEnergyGradient(coords)
print("E", E)
print("V")
print(V)
print("try a quench")
from pele.optimize import mylbfgs as quench
ret = quench(coords, lj, iprint=-1)
print("energy ", ret.energy)
print("rms gradient", ret.rms)
print("number of function calls", ret.nfev)
from pele.utils.xyz import write_xyz
printlist = []
for i in range(100):
coords = np.random.uniform(-1, 1, natoms * 3) * 2
ret = quench(coords, lj.getEnergyGradient, iprint=-1)
coords = ret.coords
X = np.reshape(coords, [natoms, 3])
com = X.sum(0) / natoms
X[:, :] -= com[np.newaxis, :]
printlist.append(np.reshape(X, natoms * 3))
with open("out.xyz", "w") as fout:
for coords in printlist:
write_xyz(fout, coords)
def testpot3():
from transition_state_refinement import guesstsLJ
pot, coords, coords1, coords2 = guesstsLJ()
coordsinit = np.copy(coords)
eigpot = LowestEigPot(coords, pot)
vec = np.random.rand(len(coords))
from pele.optimize import lbfgs_py as quench
ret = quench(vec, eigpot.getEnergyGradient, iprint=400, tol = 1e-5, maxstep = 1e-3, \
rel_energy = True)
eigval = ret[1]
eigvec = ret[0]
print "eigenvalue ", eigval
print "eigenvector", eigvec
if True:
e, g, hess = pot.getEnergyGradientHessian(coords)
u, v = np.linalg.eig(hess)
u = u.real
v = v.real
print "eigenvalues", sorted(u)
#for i in range(len(u)):
# print "eigenvalue", u[i], "eigenvector", v[:,i]
#find minimum eigenvalue, vector
imin = 0
umin = 10.
for i in range(len(u)):
if np.abs(u[i]) < 1e-10: continue
if u[i] < umin:
umin = u[i]
imin = i
#print "lowest eigenvalue ", umin, imin
#print "lowest eigenvector", v[:,imin]
trueval, truevec = u[imin], v[:,imin]
print "analytical lowest eigenvalue", trueval
maxdiff = np.max(np.abs(truevec - eigvec))
print "maximum difference between estimated and analytical eigenvectors", maxdiff, \
np.linalg.norm(eigvec), np.linalg.norm(truevec), np.dot(truevec, eigvec)
if True:
print eigvec
print truevec
def minimize(self):
"""compute the best estimate for the density of states"""
nreps = self.nrep
nbins = self.nebins
visitsT = (self.visits1d)
#print "min vis", np.min(visitsT)
#print "minlogp", np.min(self.logP)
self.reduced_energy = self.binenergy[np.newaxis, :] / (
self.Tlist[:, np.newaxis] * self.k_B)
self.whampot = WhamPotential(visitsT, self.reduced_energy)
if False:
X = np.random.rand(nreps + nbins)
else:
# estimate an initial guess for the offsets and density of states
# so the minimizer converges more rapidly
offsets_estimate, log_dos_estimate = wham_utils.estimate_dos(
self.visits1d, self.reduced_energy)
X = np.concatenate((offsets_estimate, log_dos_estimate))
E0, grad = self.whampot.getEnergyGradient(X)
rms0 = np.linalg.norm(grad) / np.sqrt(grad.size)
try:
from pele.optimize import lbfgs_cpp as quench
if self.verbose:
print "minimizing with pele lbfgs"
ret = quench(X, self.whampot, tol=1e-3, maxstep=1e4, nsteps=10000)
except ImportError:
from wham_utils import lbfgs_scipy
if self.verbose:
print "minimizing with scipy lbfgs"
ret = lbfgs_scipy(X, self.whampot, tol=1e-3, nsteps=10000)
#print "quench energy", ret.energy
if self.verbose:
print "chi^2 went from %g (rms %g) to %g (rms %g) in %d iterations" % (
E0, rms0, ret.energy, ret.rms, ret.nfev)
X = ret.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
def minimize(self):
"""compute the best estimate for the density of states"""
nreps = self.nrep
nbins = self.nebins
visitsT = (self.visits1d)
#print "min vis", np.min(visitsT)
#print "minlogp", np.min(self.logP)
self.reduced_energy = self.binenergy[np.newaxis,:] / (self.Tlist[:,np.newaxis] * self.k_B)
self.whampot = WhamPotential(visitsT, self.reduced_energy)
if False:
X = np.random.rand( nreps + nbins )
else:
# estimate an initial guess for the offsets and density of states
# so the minimizer converges more rapidly
offsets_estimate, log_dos_estimate = wham_utils.estimate_dos(self.visits1d,
self.reduced_energy)
X = np.concatenate((offsets_estimate, log_dos_estimate))
E0, grad = self.whampot.getEnergyGradient(X)
rms0 = np.linalg.norm(grad) / np.sqrt(grad.size)
try:
from pele.optimize import lbfgs_cpp as quench
if self.verbose:
print "minimizing with pele lbfgs"
ret = quench(X, self.whampot, tol=1e-3, maxstep=1e4, nsteps=10000)
except ImportError:
from wham_utils import lbfgs_scipy
if self.verbose:
print "minimizing with scipy lbfgs"
ret = lbfgs_scipy(X, self.whampot, tol=1e-3, nsteps=10000)
#print "quench energy", ret.energy
if self.verbose:
print "chi^2 went from %g (rms %g) to %g (rms %g) in %d iterations" % (
E0, rms0, ret.energy, ret.rms, ret.nfev)
X = ret.coords
self.logn_E = X[nreps:]
self.w_i_final = X[:nreps]
def main(): # pragma: no cover
#test class
natoms = 12
coords = np.random.uniform(-1,1,natoms*3)*2
lj = LJ()
E = lj.getEnergy(coords)
print "E", E
E, V = lj.getEnergyGradient(coords)
print "E", E
print "V"
print V
print "try a quench"
from pele.optimize import mylbfgs as quench
ret = quench( coords, lj, iprint=-1 )
#quench( coords, lj.getEnergyGradientNumerical, iprint=1 )
print "energy ", ret.energy
print "rms gradient", ret.rms
print "number of function calls", ret.nfev
def lineSearch(X, V, pot, aguess = 0.1, tol = 1e-3):
"""
minimize the potential along the line defined by X + a * V
i'm sure there's a better way to do this
"""
tol /= np.sqrt(len(X)) #normalize the tolerance because we're reducing dimensionality
ls = LineSearchPot(X, V, pot)
einit = pot.getEnergy(X)
#from optimize.quench import steepest_descent as quench
from pele.optimize import lbfgs_scipy as quench
a = np.zeros(1) * aguess
ret = quench(a, ls.getEnergyGradient, tol=tol)
a = ret[0][0]
e = ret[1]
funcalls = ret[3]
#print " linesearch step size", a, e, einit, e - einit, funcalls
return a, e, funcalls
def main(): # pragma: no cover
# test class
natoms = 12
coords = np.random.uniform(-1, 1, natoms * 3) * 2
lj = LJ()
E = lj.getEnergy(coords)
print("E", E)
E, V = lj.getEnergyGradient(coords)
print("E", E)
print("V")
print(V)
print("try a quench")
from pele.optimize import mylbfgs as quench
ret = quench(coords, lj, iprint=-1)
#quench( coords, lj.getEnergyGradientNumerical, iprint=1 )
print("energy ", ret.energy)
print("rms gradient", ret.rms)
print("number of function calls", ret.nfev)
def testenergy(self):
natoms = 10
coords = np.random.uniform(-1,1,natoms*3)*2
from pele.optimize import mylbfgs as quench
lj = LJ()
ret = quench(coords, lj)
coords = ret.coords
atlj = ATLJ(Z=3.)
e2 = atlj.getEnergySlow(coords)
# e1 = atlj.getEnergyWeave(coords)
# #print "%g - %g = %g" % (e1, e2, e1-e2)
# self.assertTrue( abs(e1 - e2) < 1e-12, "ATLJ: two energy methods give different results: %g - %g = %g" % (e1, e2, e1-e2) )
e1 = atlj.getEnergyFortran(coords)
#print "%g - %g = %g" % (e1, e2, e1-e2)
#print e1/e2
self.assertTrue( abs(e1 - e2) < 1e-12, "ATLJ: fortran energy gives different results: %g - %g = %g" % (e1, e2, e1-e2) )
def test():
natoms = 100
tol = 1e-6
from pele.potentials.lj import LJ
pot = LJ()
X = getInitialCoords(natoms, pot)
X += np.random.uniform(-1,1,[3*natoms]) * 0.3
#do some steepest descent steps so we don't start with a crazy structure
#from optimize.quench import _steepest_descent as steepestDescent
#ret = steepestDescent(X, pot.getEnergyGradient, iprint = 1, dx = 1e-4, nsteps = 100, gtol = 1e-3, maxstep = .5)
#X = ret[0]
#print X
Xinit = np.copy(X)
e, g = pot.getEnergyGradient(X)
print "energy", e
lbfgs = BFGS(X, pot, maxstep = 0.1)
ret = lbfgs.run(100, tol = tol, iprint=1)
print "done", ret[1], ret[2], ret[3]
print "now do the same with scipy lbfgs"
from pele.optimize import lbfgs_scipy as quench
ret = quench(Xinit, pot.getEnergyGradient, tol = tol)
print ret[1], ret[2], ret[3]
print "now do the same with scipy bfgs"
from pele.optimize import bfgs as oldbfgs
ret = oldbfgs(Xinit, pot.getEnergyGradient, tol = tol)
print ret[1], ret[2], ret[3]
print "now do the same with old gradient + linesearch"
gpl = GradientPlusLinesearch(Xinit, pot, maxstep = 0.1)
ret = gpl.run(100, tol = 1e-6)
print ret[1], ret[2], ret[3]
def testenergy(self):
natoms = 10
coords = np.random.uniform(-1, 1, natoms * 3) * 2
from pele.optimize import mylbfgs as quench
lj = LJ()
ret = quench(coords, lj)
coords = ret.coords
atlj = ATLJ(Z=3.)
e2 = atlj.getEnergySlow(coords)
# e1 = atlj.getEnergyWeave(coords)
# #print "%g - %g = %g" % (e1, e2, e1-e2)
# self.assertTrue( abs(e1 - e2) < 1e-12, "ATLJ: two energy methods give different results: %g - %g = %g" % (e1, e2, e1-e2) )
e1 = atlj.getEnergyFortran(coords)
#print "%g - %g = %g" % (e1, e2, e1-e2)
#print e1/e2
self.assertTrue(
abs(e1 - e2) < 1e-12,
"ATLJ: fortran energy gives different results: %g - %g = %g" %
(e1, e2, e1 - e2))
def test_soft_sphere(natoms=9):
rho = 1.6
boxl = 1.
meandiam = boxl / (float(natoms) / rho)**(1. / 3)
print "mean diameter", meandiam
#set up potential
diams = np.array([meandiam
for i in range(natoms)]) #make them all the same
pot = SoftSphere(diams=diams)
#initial coordinates
coords = np.random.uniform(-1, 1, [natoms * 3]) * (natoms)**(1. / 3)
print len(coords)
E = pot.getEnergy(coords)
print "initial energy", E
printlist = []
printlist.append((coords.copy(), "intial coords"))
#test a quench with default lbfgs
from pele.optimize import mylbfgs as quench
res = quench(coords, pot, iprint=-1)
printlist.append((res.coords.copy(), "intial coords"))
print "energy post quench", pot.getEnergy(coords)
fname = "out.xyz"
print "saving coordinates to", fname
from pele.utils.xyz import write_xyz
with open(fname, "w") as fout:
for xyz, line2 in printlist:
xyz = putInBox(xyz, boxl)
write_xyz(fout, xyz, title=line2)
from scipy.optimize import check_grad
res = check_grad(pot.getEnergy, pot.getGradient, coords)
print "testing gradient (should be small)", res
def test_soft_sphere(natoms = 9):
rho = 1.6
boxl = 1.
meandiam = boxl / (float(natoms)/rho)**(1./3)
print "mean diameter", meandiam
#set up potential
diams = np.array([meandiam for i in range(natoms)]) #make them all the same
pot = SoftSphere(diams = diams)
#initial coordinates
coords = np.random.uniform(-1,1,[natoms*3]) * (natoms)**(1./3)
print len(coords)
E = pot.getEnergy(coords)
print "initial energy", E
printlist = []
printlist.append((coords.copy(), "intial coords"))
#test a quench with default lbfgs
from pele.optimize import mylbfgs as quench
res = quench(coords, pot, iprint=-1)
printlist.append((res.coords.copy(), "intial coords"))
print "energy post quench", pot.getEnergy(coords)
fname = "out.xyz"
print "saving coordinates to", fname
from pele.utils.xyz import write_xyz
with open(fname, "w") as fout:
for xyz,line2 in printlist:
xyz = putInBox(xyz, boxl)
write_xyz(fout, xyz, title=line2)
from scipy.optimize import check_grad
res = check_grad(pot.getEnergy, pot.getGradient, coords)
print "testing gradient (should be small)", res
coords = np.random.uniform(-1,1,[natoms*3]) * (natoms)**(1./3)
E = pot.getEnergy(coords)
print "initial energy", E
#set up quench routine
#from optimize.quench import fire as quench
#from optimize.quench import cg as quench
from pele.optimize import lbfgs_scipy as quench #numpy lbfgs routine
#from optimize.quench import fmin as quench
#from optimize.quench import steepest_descent as quench
#start from quenched coordinates
ret = quench(coords, pot.getEnergyGradient)
coords = ret[0]
#set up functions to pass to basin hopping
#set up the step taking routine
#Normal basin hopping takes each step from the quenched coords. This modified step taking routine takes a step from the
#last accepted coords, not from the quenched coords
from pele.take_step.random_displacement import takeStep
takestep = takeStep(stepsize=.01)
#pass a function which rejects the step if the system leaved the inital basin.
import do_quenching
def minimize(pot, coords0):
from pele.optimize import lbfgs_cpp as quench
return quench(coords0, pot, iprint=1, tol=1.0e-3, nsteps=100)
if self.count % self.printfrq == 0:
self.center(coords)
write_xyz(self.fout, coords, title=str(E))
self.count += 1
#def center(E, coords, accepted):
# c = np.reshape()
natoms = 40
coords = np.random.rand(natoms*3)
lj = LJ()
ret = quench(coords, lj)
coords = ret.coords
takestep = TakeStep(stepsize=0.1 )
#do equilibration steps, adjusting stepsize
tsadapt = AdaptiveStepsize(takestep)
mc = MonteCarlo(coords, lj, tsadapt, temperature = 0.5)
equilout = open("equilibration","w")
#mc.outstream = equilout
mc.setPrinting(equilout, 1)
mc.run(10000)
#fix stepsize and do production run
mc.takeStep = takestep
mcout = open("mc.out", "w")
xyz2 = neb.coords[i+1,:]
dist = np.linalg.norm(xyz1 - xyz2)
E = getEnergy(xyz1)
fout.write( str(S) + " " + str(E) + "\n")
S += dist
xyz = neb.coords[-1,:]
E = getEnergy(xyz)
fout.write( str(S) + " " + str(E) + "\n")
lj = LJ()
natoms = 17
X1 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
ret = quench( X1, lj.getEnergyGradient)
X1 = ret[0]
X2 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
ret = quench( X2, lj.getEnergyGradient)
X2 = ret[0]
dist, X1, X2 = minpermdist( X1, X2, niter = 100 )
distf = np.linalg.norm(X1 - X2)
print "dist returned ", dist
print "dist from structures ", distf
#X1 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 0., 1.,] )
#X2 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 1., 0.,] )
import copy
X1i = copy.copy(X1)
X2i = copy.copy(X2)
def runptmc(nsteps_tot=100000):
natoms = 31
nreplicas = 4
Tmin = 0.2
Tmax = 0.4
nsteps_equil = 10000
nsteps_tot = 100000
histiprint = nsteps_tot / 10
exchange_frq = 100 * nreplicas
coords = np.random.random(3 * natoms)
#quench the coords so we start from a reasonable location
mypot = lj.LJ()
ret = quench(coords, mypot)
coords = ret.coords
Tlist = getTemps(Tmin, Tmax, nreplicas)
replicas = []
ostreams = []
histograms = []
takesteplist = []
radius = 2.5
# create all the replicas which will be passed to PTMC
for i in range(nreplicas):
T = Tlist[i]
potential = lj.LJ()
takestep = RandomDisplacement(stepsize=0.01)
adaptive = AdaptiveStepsize(takestep, last_step=nsteps_equil)
takesteplist.append(adaptive)
file = "mcout." + str(i + 1)
ostream = open(file, "w")
hist = EnergyHistogram(-134., 10., 1000)
histograms.append(hist)
event_after_step = [hist]
radiustest = SphericalContainer(radius)
accept_tests = [radiustest]
mc = MonteCarlo(coords, potential, takeStep=takestep, temperature=T, \
outstream=ostream, event_after_step = event_after_step, \
confCheck = accept_tests)
mc.histogram = hist #for convienence
mc.printfrq = 1
replicas.append(mc)
#is it possible to pickle a mc object?
#cp = copy.deepcopy(replicas[0])
#import pickle
#with open("mc.pickle", "w") as fout:
#pickle.dump(takesteplist[0], fout)
#attach an event to print xyz coords
from pele.printing.print_atoms_xyz import PrintEvent
printxyzlist = []
for n, rep in enumerate(replicas):
outf = "dumpstruct.%d.xyz" % (n + 1)
printxyz = PrintEvent(outf, frq=500)
printxyzlist.append(printxyz)
rep.addEventAfterStep(printxyz)
#attach an event to print histograms
for n, rep in enumerate(replicas):
outf = "hist.%d" % (n + 1)
histprint = PrintHistogram(outf, rep.histogram, histiprint)
rep.addEventAfterStep(histprint)
ptmc = PTMC(replicas)
ptmc.use_independent_exchange = True
ptmc.exchange_frq = exchange_frq
ptmc.run(nsteps_tot)
#do production run
#fix the step sizes
#for takestep in takesteplist:
# takestep.useFixedStep()
#ptmc.run(30000)
if False: #this doesn't work
print "final energies"
for rep in ptmc.replicas:
print rep.temperature, rep.markovE
for rep in ptmc.replicas_par:
print rep.mcsys.markovE
for k in range(nreplicas):
e, T = ptmc.getRepEnergyT(k)
print T, e
if False: #this doesn't work
print "histograms"
for i, hist in enumerate(histograms):
fname = "hist." + str(i)
print fname
with open(fname, "w") as fout:
for (e, visits) in hist:
fout.write("%g %d\n" % (e, visits))
ptmc.end() #close the open threads
def get_minimizer(self, **kwargs):
from pele.optimize import lbfgs_cpp as quench
return lambda coords: quench(coords, self.get_potential(),tol=0.00001,**kwargs)
def myMinimizer(coords,pot,**kwargs):
from pele.optimize import lbfgs_cpp as quench
#print coords
return quench(coords,pot,**kwargs)
def runptmc(nsteps_tot = 100000):
natoms = 31
nreplicas = 4
Tmin = 0.2
Tmax = 0.4
nsteps_equil = 10000
nsteps_tot = 100000
histiprint = nsteps_tot / 10
exchange_frq = 100*nreplicas
coords=np.random.random(3*natoms)
#quench the coords so we start from a reasonable location
mypot = lj.LJ()
ret = quench(coords, mypot)
coords = ret.coords
Tlist = getTemps(Tmin, Tmax, nreplicas)
replicas = []
ostreams = []
histograms = []
takesteplist = []
radius = 2.5
# create all the replicas which will be passed to PTMC
for i in range(nreplicas):
T = Tlist[i]
potential = lj.LJ()
takestep = RandomDisplacement( stepsize=0.01)
adaptive = AdaptiveStepsize(takestep, last_step = nsteps_equil)
takesteplist.append( adaptive )
file = "mcout." + str(i+1)
ostream = open(file, "w")
hist = EnergyHistogram( -134., 10., 1000)
histograms.append(hist)
event_after_step=[hist]
radiustest = SphericalContainer(radius)
accept_tests = [radiustest]
mc = MonteCarlo(coords, potential, takeStep=takestep, temperature=T, \
outstream=ostream, event_after_step = event_after_step, \
confCheck = accept_tests)
mc.histogram = hist #for convienence
mc.printfrq = 1
replicas.append(mc)
#is it possible to pickle a mc object?
#cp = copy.deepcopy(replicas[0])
#import pickle
#with open("mc.pickle", "w") as fout:
#pickle.dump(takesteplist[0], fout)
#attach an event to print xyz coords
from pele.printing.print_atoms_xyz import PrintEvent
printxyzlist = []
for n, rep in enumerate(replicas):
outf = "dumpstruct.%d.xyz" % (n+1)
printxyz = PrintEvent(outf, frq=500)
printxyzlist.append( printxyz)
rep.addEventAfterStep(printxyz)
#attach an event to print histograms
for n, rep in enumerate(replicas):
outf = "hist.%d" % (n+1)
histprint = PrintHistogram(outf, rep.histogram, histiprint)
rep.addEventAfterStep(histprint)
ptmc = PTMC(replicas)
ptmc.use_independent_exchange = True
ptmc.exchange_frq = exchange_frq
ptmc.run(nsteps_tot)
#do production run
#fix the step sizes
#for takestep in takesteplist:
# takestep.useFixedStep()
#ptmc.run(30000)
if False: #this doesn't work
print "final energies"
for rep in ptmc.replicas:
print rep.temperature, rep.markovE
for rep in ptmc.replicas_par:
print rep.mcsys.markovE
for k in range(nreplicas):
e,T = ptmc.getRepEnergyT(k)
print T, e
if False: #this doesn't work
print "histograms"
for i,hist in enumerate(histograms):
fname = "hist." + str(i)
print fname
with open(fname, "w") as fout:
for (e, visits) in hist:
fout.write( "%g %d\n" % (e, visits) )
ptmc.end() #close the open threads
def myMinimizer(coords, pot, **kwargs):
from pele.optimize import lbfgs_cpp as quench
#print coords
return quench(coords, pot, **kwargs)
#initial coordinates coords = np.random.uniform(-1,1,[natoms*3]) * (natoms)**(1./3) E = pot.getEnergy(coords) print "initial energy", E printlist = [] #list of coordinates saved for printing printlist.append((coords.copy(), "intial coords")) #test a quench with default lbfgs #from optimize.quench import quench from pele.optimize import lbfgs_ase as quench coords, E, rms, funcalls = quench(coords, pot.getEnergyGradient, iprint=1) printlist.append((coords.copy(), "intial coords")) print "energy post quench", pot.getEnergy(coords) from scipy.optimize import check_grad res = check_grad(pot.getEnergy, pot.getGradient, coords) print "testing gradient (should be small)", res fname = "out.xyz" print "saving coordinates to", fname from pele.utils.xyz import write_xyz
def testpot1():
from pele.potentials.lj import LJ
import itertools
pot = LJ()
a = 1.12 #2.**(1./6.)
theta = 60./360*np.pi
coords = [ 0., 0., 0., \
-a, 0., 0., \
-a/2, a*np.cos(theta), 0., \
-a/2, -a*np.cos(theta), 0.1 \
]
natoms = len(coords)/3
c = np.reshape(coords, [-1,3])
for i, j in itertools.combinations(range(natoms), 2):
r = np.linalg.norm(c[i,:] - c[j,:])
print i, j, r
e, g = pot.getEnergyGradient(coords)
print "initial E", e
print "initial G", g, np.linalg.norm(g)
eigpot = LowestEigPot(coords, pot)
vec = np.random.rand(len(coords))
e, g = eigpot.getEnergyGradient(vec)
print "eigenvalue", e
print "eigenvector", g
if True:
e, g, hess = pot.getEnergyGradientHessian(coords)
print "shape hess", np.shape(hess)
print "hessian", hess
u, v = np.linalg.eig(hess)
print "max imag value", np.max(np.abs(u.imag))
print "max imag vector", np.max(np.abs(v.imag))
u = u.real
v = v.real
print "eigenvalues", u
for i in range(len(u)):
print "eigenvalue", u[i], "eigenvector", v[:,i]
#find minimum eigenvalue, vector
imin = 0
umin = 10.
for i in range(len(u)):
if np.abs(u[i]) < 1e-10: continue
if u[i] < umin:
umin = u[i]
imin = i
print "lowest eigenvalue ", umin, imin
print "lowest eigenvector", v[:,imin]
from pele.optimize import lbfgs_py as quench
ret = quench(vec, eigpot.getEnergyGradient, iprint=10, tol = 1e-5, maxstep = 1e-3, \
rel_energy = True)
print ret
print "lowest eigenvalue "
print umin, imin
print "lowest eigenvector"
print v[:,imin]
print "now the estimate"
print ret[1]
print ret[0]