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 lbfgs_py(coords, pot, **kwargs):
if not hasattr(pot, "getEnergyGradient"):
# for compatibility with old quenchers.
# assume pot is a getEnergyGradient function
pot = _getEnergyGradientWrapper(pot)
lbfgs = LBFGS(coords, pot, **kwargs)
return lbfgs.run()
def setUp1(self, verbose=False, **kwargs):
np.random.seed(0)
natoms = 18
self.system = LJCluster(natoms)
self.pot = self.system.get_potential()
x = self.system.get_random_configuration()
ret = lbfgs_py(x, self.pot, tol=10)
self.x = ret.coords
self.kwargs = kwargs
self.verbose = verbose
self.M = 4
if self.verbose: iprint = 1
else: iprint = -1
self.myo = MYLBFGS(self.x,
self.pot,
iprint=iprint,
debug=True,
M=self.M)
self.o = LBFGS(self.x,
self.pot,
iprint=iprint,
debug=True,
M=self.M,
**self.kwargs)
def test1(self):
pot = DiscontinuousHarmonic()
x0 = np.array([-10, 1])
opt = LBFGS(x0, pot, debug=True)
print('this runnnns')
res = opt.run()
self.assertFalse(res.success)
def test_event(self):
self.called = False
def event(coords=None, energy=None, rms=None):
self.called = True
opt = LBFGS(self.x0, self.pot, events=[event])
opt.one_iteration()
self.assertTrue(self.called)
def _lbfgs_py(coords, pot, **kwargs):
lbfgs = LBFGS(coords, pot, **kwargs)
ret = lbfgs.run()
coords = ret.coords
e = ret.energy
rms = ret.rms
funcalls = ret.nfev
return coords, e, rms, funcalls, ret
def test_event(self):
self.called = False
def event(coords=None, energy=None, rms=None):
self.called = True
opt = LBFGS(self.x0, self.pot, events=[event])
opt.one_iteration()
self.assertTrue(self.called)
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, fortran=True, debug=True)
ret = minimizer.run()
m2 = LBFGS(self.x.copy(), self.pot, fortran=False, debug=True)
ret2 = m2.run()
print "fortran", ret.nfev, ret2.nfev
# self.assertEqual(ret.nfev, ret2.nfev)
self.assertAlmostEqual(ret.energy, ret2.energy, 5)
def __init__(self, coords, potential, eigenvec, energy=None, gradient=None, **minimizer_kwargs):
self.tspot = _TransversePotential(potential, eigenvec)
if energy is not None and gradient is not None:
transverse_energy, transverse_gradient = self.tspot.projected_energy_gradient(energy, gradient)
else:
transverse_energy, transverse_gradient = None, None
self.walker = LBFGS(coords, self.tspot,
energy=transverse_energy, gradient=transverse_gradient,
**minimizer_kwargs)
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, armijo=True, debug=True)
ret = minimizer.run()
self.assertTrue(ret.success)
print "\n\n"
minimizer = LBFGS(self.x.copy(), self.pot, armijo=False, debug=True)
ret_nowolfe = minimizer.run()
self.assertTrue(ret_nowolfe.success)
print "nfev armijo, noarmijo", ret.nfev, ret_nowolfe.nfev, ret.energy, ret_nowolfe.energy
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, debug=True)
minimizer._use_wolfe = True
ret = minimizer.run()
self.assertTrue(ret.success)
print "\n\n"
minimizer = LBFGS(self.x.copy(), self.pot, debug=True)
ret_nowolfe = minimizer.run()
self.assertTrue(ret_nowolfe.success)
print "nfev wolfe, nowolfe", ret.nfev, ret_nowolfe.nfev, ret.energy, ret_nowolfe.energy
def run(X_train):
# fit a Gaussian Mixture Model with two components
clf = mixture.GMM(n_components=2, covariance_type='full')
pot = GMMPotential(clf, X_train)
params = pot.get_random_coords()
print params
e, g = pot.getEnergyGradient(params)
print "energy", e
print "grad", g
opt = LBFGS(params, pot, tol=1e-5, maxstep=1., iprint=1)#, events=[print_event])
res = opt.run()
print "finished"
e, g = pot.getEnergyGradient(res.coords)
print "energy", e
print "grad"
print "grad", g
# raise Exception("exiting early")
# clf.fit(X_train)
print "weights"
print clf.covars_
print "\nmeans"
print clf.means_
print "\ncovariances"
print clf.covars_
# display predicted scores by the model as a contour plot
x = np.linspace(-20.0, 30.0)
y = np.linspace(-20.0, 40.0)
X, Y = np.meshgrid(x, y)
XX = np.array([X.ravel(), Y.ravel()]).T
Z = -clf.score_samples(XX)[0]
Z = Z.reshape(X.shape)
CS = plt.contour(X, Y, Z, norm=LogNorm(vmin=1.0, vmax=1000.0),
levels=np.logspace(0, 3, 10))
CB = plt.colorbar(CS, shrink=0.8, extend='both')
plt.scatter(X_train[:, 0], X_train[:, 1], .8)
plt.title('Negative log-likelihood predicted by a GMM')
plt.axis('tight')
make_ellipses(clf, plt.gca())
plt.show()
def __init__(self, coords, potential, eigenvec,
quenchRoutine=None, **minimizer_kwargs):
self.dimer_potential = _DimerPotential(potential, eigenvec)
if quenchRoutine:
self.minimizer = quenchRoutine(coords, self.dimer_potential, **minimizer_kwargs)
else:
self.minimizer = LBFGS(coords, self.dimer_potential, **minimizer_kwargs)
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, debug=True)
minimizer._cython = True
ret = minimizer.run()
m2 = LBFGS(self.x.copy(), self.pot, debug=True)
minimizer._cython = True
ret2 = m2.run()
print("cython", ret.nfev, ret2.nfev)
self.assertEqual(ret.nfev, ret2.nfev)
self.assertAlmostEqual(ret.energy, ret2.energy, 5)
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, debug=True)
minimizer._use_wolfe = True
ret = minimizer.run()
self.assertTrue(ret.success)
print "\n\n"
minimizer = LBFGS(self.x.copy(), self.pot, debug=True)
ret_nowolfe = minimizer.run()
self.assertTrue(ret_nowolfe.success)
print "nfev wolfe, nowolfe", ret.nfev, ret_nowolfe.nfev, ret.energy, ret_nowolfe.energy
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, fortran=True, debug=True)
ret = minimizer.run()
m2 = LBFGS(self.x.copy(), self.pot, fortran=False, debug=True)
ret2 = m2.run()
print("fortran", ret.nfev, ret2.nfev)
# self.assertEqual(ret.nfev, ret2.nfev)
self.assertAlmostEqual(ret.energy, ret2.energy, 5)
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, debug=True)
minimizer._cython = True
ret = minimizer.run()
m2 = LBFGS(self.x.copy(), self.pot, debug=True)
minimizer._cython = True
ret2 = m2.run()
print "cython", ret.nfev, ret2.nfev
self.assertEqual(ret.nfev, ret2.nfev)
self.assertAlmostEqual(ret.energy, ret2.energy, 5)
def setUp1(self, verbose=False, **kwargs):
np.random.seed(0)
natoms = 18
self.system = LJCluster(natoms)
self.pot = self.system.get_potential()
x = self.system.get_random_configuration()
ret = lbfgs_py(x, self.pot, tol=10)
self.x = ret.coords
self.kwargs = kwargs
self.verbose = verbose
self.M = 4
if self.verbose: iprint=1
else: iprint = -1
self.myo = MYLBFGS(self.x, self.pot, iprint=iprint, debug=True, M=self.M)
self.o = LBFGS(self.x, self.pot, iprint=iprint, debug=True, M=self.M, **self.kwargs)
class TestLBFGS_State(unittest.TestCase):
def setUp(self):
self.system = LJCluster(13)
self.x = self.system.get_random_configuration()
self.pot = self.system.get_potential()
self.minimizer = LBFGS(self.x, self.pot)
def test_state(self):
# do several minimization iterations
for i in xrange(10):
self.minimizer.one_iteration()
# get the state and save it
ret = self.minimizer.get_result()
state = self.minimizer.get_state()
x1 = ret.coords.copy()
# do several more iteration steps
for i in xrange(10):
self.minimizer.one_iteration()
# now make a new minimizer and do several iterations
minimizer2 = LBFGS(x1, self.pot)
minimizer2.set_state(state)
for i in xrange(10):
minimizer2.one_iteration()
# test that the two minimizers are in the same state
ret1 = self.minimizer.get_result()
ret2 = minimizer2.get_result()
self.assertEqual(ret1.energy, ret2.energy)
self.assertTrue((ret1.coords == ret2.coords).all())
state1 = self.minimizer.get_state()
state2 = minimizer2.get_state()
self.assertTrue((state1.y == state2.y).all())
self.assertTrue((state1.s == state2.s).all())
self.assertTrue((state1.rho == state2.rho).all())
self.assertTrue((state1.dXold == state2.dXold).all())
self.assertTrue((state1.dGold == state2.dGold).all())
self.assertEqual(state1.H0, state2.H0)
self.assertEqual(state1.k, state2.k)
def test(self):
minimizer = LBFGS(self.x.copy(), self.pot, armijo=True, debug=True)
ret = minimizer.run()
self.assertTrue(ret.success)
print "\n\n"
minimizer = LBFGS(self.x.copy(), self.pot, armijo=False, debug=True)
ret_nowolfe = minimizer.run()
self.assertTrue(ret_nowolfe.success)
self.assertAlmostEqual(ret.energy, ret_nowolfe.energy, delta=1e-3)
print "nfev armijo, noarmijo", ret.nfev, ret_nowolfe.nfev, ret.energy, ret_nowolfe.energy
def test_state(self):
# do several minimization iterations
for i in range(10):
self.minimizer.one_iteration()
# get the state and save it
ret = self.minimizer.get_result()
state = self.minimizer.get_state()
x1 = ret.coords.copy()
# do several more iteration steps
for i in range(10):
self.minimizer.one_iteration()
# now make a new minimizer and do several iterations
minimizer2 = LBFGS(x1, self.pot)
minimizer2.set_state(state)
for i in range(10):
minimizer2.one_iteration()
# test that the two minimizers are in the same state
ret1 = self.minimizer.get_result()
ret2 = minimizer2.get_result()
self.assertEqual(ret1.energy, ret2.energy)
self.assertTrue((ret1.coords == ret2.coords).all())
state1 = self.minimizer.get_state()
state2 = minimizer2.get_state()
self.assertTrue((state1.y == state2.y).all())
self.assertTrue((state1.s == state2.s).all())
self.assertTrue((state1.rho == state2.rho).all())
self.assertTrue((state1.dXold == state2.dXold).all())
self.assertTrue((state1.dGold == state2.dGold).all())
self.assertEqual(state1.H0, state2.H0)
self.assertEqual(state1.k, state2.k)
def test_state(self):
# do several minimization iterations
for i in xrange(10):
self.minimizer.one_iteration()
# get the state and save it
ret = self.minimizer.get_result()
state = self.minimizer.get_state()
x1 = ret.coords.copy()
# do several more iteration steps
for i in xrange(10):
self.minimizer.one_iteration()
# now make a new minimizer and do several iterations
minimizer2 = LBFGS(x1, self.pot)
minimizer2.set_state(state)
for i in xrange(10):
minimizer2.one_iteration()
# test that the two minimizers are in the same state
ret1 = self.minimizer.get_result()
ret2 = minimizer2.get_result()
self.assertEqual(ret1.energy, ret2.energy)
self.assertTrue((ret1.coords == ret2.coords).all())
state1 = self.minimizer.get_state()
state2 = minimizer2.get_state()
self.assertTrue((state1.y == state2.y).all())
self.assertTrue((state1.s == state2.s).all())
self.assertTrue((state1.rho == state2.rho).all())
self.assertTrue((state1.dXold == state2.dXold).all())
self.assertTrue((state1.dGold == state2.dGold).all())
self.assertEqual(state1.H0, state2.H0)
self.assertEqual(state1.k, state2.k)
class _TransverseWalker(object):
"""It minimizes the energy in the direction perpendicular to a vector
this class manages the minimization _TransversePotential
Parameters
----------
coords : float array
the starting coordinates
potential : Potential object
eigenvec : float array
energy will be minimized in the direction perpendicular to this vector
energy, gradient : float and float array
the energy and gradient at position coords
minimizer_kwargs : kwargs
these kwargs are passed to the minimizer
"""
def __init__(self, coords, potential, eigenvec, energy=None, gradient=None, **minimizer_kwargs):
self.tspot = _TransversePotential(potential, eigenvec)
if energy is not None and gradient is not None:
transverse_energy, transverse_gradient = self.tspot.projected_energy_gradient(energy, gradient)
else:
transverse_energy, transverse_gradient = None, None
self.walker = LBFGS(coords, self.tspot,
energy=transverse_energy, gradient=transverse_gradient,
**minimizer_kwargs)
def update_eigenvec(self, eigenvec, eigenval):
"""update the vecotr"""
self.tspot.update_vector(eigenvec)
def update_maxstep(self, maxstep):
"""update the maximum step size of the minimizer"""
self.walker.maxstep = float(maxstep)
def update_coords(self, coords, true_energy, true_gradient):
"""update the position of the optimizer
this must be called after update_eigenvec
"""
energy, gradient = self.tspot.projected_energy_gradient(true_energy, true_gradient)
self.walker.update_coords(coords, energy, gradient)
def stop_criterion_satisfied(self):
"""test if the stop criterion is satisfied"""
return self.walker.stop_criterion_satisfied()
def get_true_energy_gradient(self, coords):
"""return the true energy and gradient"""
return self.tspot.get_true_energy_gradient(coords)
# def get_energy(self):
# """return the true energy
#
# warning it's possible for this to return the wrong energy if the minimizer
# had an aborted line search on the last iteration.
# """
# return self.tspot.true_energy
#
# def get_gradient(self):
# """return the true gradient
#
# warning it's possible for this to return the wrong energy if the minimizer
# had an aborted line search on the last iteration.
# """
# return self.tspot.true_gradient
def get_result(self):
"""return the results object"""
ret = self.walker.get_result()
ret.nfev = self.tspot.nfev
return ret
def run(self, niter):
"""do a specified number of iterations, or until the stop criterion is satisfied"""
for i in range(niter):
if self.stop_criterion_satisfied():
break
self.walker.one_iteration()
return self.get_result()
class TestLBFGS_State(unittest.TestCase):
def setUp(self):
self.system = LJCluster(13)
self.x = self.system.get_random_configuration()
self.pot = self.system.get_potential()
self.minimizer = LBFGS(self.x, self.pot)
def test_state(self):
# do several minimization iterations
for i in xrange(10):
self.minimizer.one_iteration()
# get the state and save it
ret = self.minimizer.get_result()
state = self.minimizer.get_state()
x1 = ret.coords.copy()
# do several more iteration steps
for i in xrange(10):
self.minimizer.one_iteration()
# now make a new minimizer and do several iterations
minimizer2 = LBFGS(x1, self.pot)
minimizer2.set_state(state)
for i in xrange(10):
minimizer2.one_iteration()
# test that the two minimizers are in the same state
ret1 = self.minimizer.get_result()
ret2 = minimizer2.get_result()
self.assertEqual(ret1.energy, ret2.energy)
self.assertTrue((ret1.coords == ret2.coords).all())
state1 = self.minimizer.get_state()
state2 = minimizer2.get_state()
self.assertTrue((state1.y == state2.y).all())
self.assertTrue((state1.s == state2.s).all())
self.assertTrue((state1.rho == state2.rho).all())
self.assertTrue((state1.dXold == state2.dXold).all())
self.assertTrue((state1.dGold == state2.dGold).all())
self.assertEqual(state1.H0, state2.H0)
self.assertEqual(state1.k, state2.k)
def test_reset(self):
# do several minimization iterations
m1 = LBFGS(self.x, self.pot)
for i in xrange(10):
m1.one_iteration()
# reset the minimizer and do it again
m1.reset()
e, g = self.pot.getEnergyGradient(self.x)
m1.update_coords(self.x, e, g)
for i in xrange(10):
m1.one_iteration()
# do the same number of steps of a new minimizer
m2 = LBFGS(self.x, self.pot)
for i in xrange(10):
m2.one_iteration()
# they should be the same (more or less)
n = min(m1.k, m1.M)
self.assertAlmostEqual(m1.H0, m2.H0, 5)
self.assertEqual(m1.k, m2.k)
arrays_nearly_equal(self, m1.y[:n, :], m2.y[:n, :])
arrays_nearly_equal(self, m1.s[:n, :], m2.s[:n, :])
arrays_nearly_equal(self, m1.rho[:n], m2.rho[:n])
res1 = m1.get_result()
res2 = m2.get_result()
self.assertNotEqual(res1.nfev, res2.nfev)
self.assertNotEqual(res1.nsteps, res2.nsteps)
self.assertAlmostEqual(res1.energy, res2.energy)
arrays_nearly_equal(self, res1.coords, res2.coords)
def reset(self):
LBFGS.reset(self)
self._iter = 0
def lbfgs_py(coords, pot, **kwargs):
lbfgs = LBFGS(coords, pot, **kwargs)
return lbfgs.run()
def lbfgs_py(coords, pot, **kwargs):
lbfgs = LBFGS(coords, pot, **kwargs)
return lbfgs.run()
def test1(self):
pot = DiscontinuousHarmonic()
x0 = np.array([-10, 1])
opt = LBFGS(x0, pot, debug=True)
res = opt.run()
self.assertFalse(res.success)
class TestMYLBFGS_LBFGS(unittest.TestCase):
def setUp(self):
self.setUp1(verbose=False)
def setUp1(self, verbose=False, **kwargs):
np.random.seed(0)
natoms = 18
self.system = LJCluster(natoms)
self.pot = self.system.get_potential()
x = self.system.get_random_configuration()
ret = lbfgs_py(x, self.pot, tol=10)
self.x = ret.coords
self.kwargs = kwargs
self.verbose = verbose
self.M = 4
if self.verbose: iprint=1
else: iprint = -1
self.myo = MYLBFGS(self.x, self.pot, iprint=iprint, debug=True, M=self.M)
self.o = LBFGS(self.x, self.pot, iprint=iprint, debug=True, M=self.M, **self.kwargs)
def test(self):
N = self.x.size
M = self.M
myo = self.myo
o = self.o
# do one iteration
for i in xrange(3 * self.M):
myo.one_iteration()
o.one_iteration()
if self.verbose:
print ""
print "H0", myo.H0, o.H0
print "rho ", o.rho[:]
print "myrho", myo.W[N:N+M]
myret = myo.get_result()
ret = o.get_result()
self.assertAlmostEqual(ret.energy, myret.energy, 4)
self.assertLess(np.max(np.abs(myret.coords - ret.coords)), 1e-6)
# do a second iteration
for i in xrange(1):
myo.one_iteration()
o.one_iteration()
myret = myo.get_result()
ret = o.get_result()
if self.verbose:
print "H0", myret.H0, ret.H0
print "rho ", o.rho[:]
print "myrho", myo.W[N:N+M]
self.assertAlmostEqual(ret.energy, myret.energy, 4)
self.assertLess(np.max(np.abs(myret.coords - ret.coords)), 1e-6)
def test_complete(self):
myret = self.myo.run()
ret = self.o.run()
self.assertEqual(ret.nfev, myret.nfev)
self.assertEqual(ret.nsteps, myret.nsteps)
self.assertAlmostEqual(ret.energy, myret.energy, 4)
self.assertLess(np.max(np.abs(myret.coords - ret.coords)), 1e-6)
def __init__(self, coords, potential, eigenvec, **minimizer_kwargs):
self.dimer_potential = _DimerPotential(potential, eigenvec)
self.minimizer = LBFGS(coords, self.dimer_potential,
**minimizer_kwargs)
class _DimerTranslator(object):
"""object to manage the translation of the dimer using an optimization algorithm
Parameters
----------
coords : float array
the starting point of the dimer
potential : Potential object
eigenvec : float array
the initial direction along which the dimer lies
minimizer_kwargs : kwargs
these kwargs are passed to the optimizer
"""
def __init__(self, coords, potential, eigenvec, **minimizer_kwargs):
self.dimer_potential = _DimerPotential(potential, eigenvec)
self.minimizer = LBFGS(coords, self.dimer_potential, **minimizer_kwargs)
def stop_criterion_satisfied(self):
"""test if the stop criterion is satisfied"""
return self.minimizer.stop_criterion_satisfied()
def get_true_energy_gradient(self, coords):
"""return the true energy and gradient"""
return self.dimer_potential.get_true_energy_gradient(coords)
# def get_energy(self):
# """return the true energy"""
# return self.dimer_potential.true_energy
#
# def get_gradient(self):
# """return the true gradient"""
# return self.dimer_potential.true_gradient
def update_eigenvec(self, eigenvec, eigenval):
"""update the direction (rotation) of the dimer"""
self.dimer_potential.update_eigenvec(eigenvec)
def update_coords(self, coords, true_energy, true_gradient):
"""update the position of the dimer
this must be called after update_eigenvec
"""
energy, gradient = self.dimer_potential.projected_energy_gradient(true_energy, true_gradient)
self.minimizer.update_coords(coords, energy, gradient)
def update_maxstep(self, maxstep):
"""change the maximum step size of the optimizer"""
self.minimizer.maxstep = float(maxstep)
def run(self, niter):
"""do a specified number of iterations, or until the stop criterion is satisfied"""
for i in xrange(niter):
if self.stop_criterion_satisfied():
break
self.minimizer.one_iteration()
return self.get_result()
def get_result(self):
"""return the results object"""
return self.minimizer.get_result()
def projected_energy_gradient(self, energy, gradient):
"""return the projected energy and gradient"""
return self.dimer_potential.projected_energy_gradient(energy, gradient)
def test_reset(self):
# do several minimization iterations
m1 = LBFGS(self.x, self.pot)
for i in xrange(10):
m1.one_iteration()
# reset the minimizer and do it again
m1.reset()
e, g = self.pot.getEnergyGradient(self.x)
m1.update_coords(self.x, e, g)
for i in xrange(10):
m1.one_iteration()
# do the same number of steps of a new minimizer
m2 = LBFGS(self.x, self.pot)
for i in xrange(10):
m2.one_iteration()
# they should be the same (more or less)
n = min(m1.k, m1.M)
self.assertAlmostEqual(m1.H0, m2.H0, 5)
self.assertEqual(m1.k, m2.k)
arrays_nearly_equal(self, m1.y[:n, :], m2.y[:n, :])
arrays_nearly_equal(self, m1.s[:n, :], m2.s[:n, :])
arrays_nearly_equal(self, m1.rho[:n], m2.rho[:n])
res1 = m1.get_result()
res2 = m2.get_result()
self.assertNotEqual(res1.nfev, res2.nfev)
self.assertNotEqual(res1.nsteps, res2.nsteps)
self.assertAlmostEqual(res1.energy, res2.energy)
arrays_nearly_equal(self, res1.coords, res2.coords)
def __init__(self, coords, potential, eigenvec, **minimizer_kwargs):
self.dimer_potential = _DimerPotential(potential, eigenvec)
self.minimizer = LBFGS(coords, self.dimer_potential, **minimizer_kwargs)
class TestLBFGS_State(unittest.TestCase):
def setUp(self):
self.system = LJCluster(13)
self.x = self.system.get_random_configuration()
self.pot = self.system.get_potential()
self.minimizer = LBFGS(self.x, self.pot)
def test_state(self):
# do several minimization iterations
for i in range(10):
self.minimizer.one_iteration()
# get the state and save it
ret = self.minimizer.get_result()
state = self.minimizer.get_state()
x1 = ret.coords.copy()
# do several more iteration steps
for i in range(10):
self.minimizer.one_iteration()
# now make a new minimizer and do several iterations
minimizer2 = LBFGS(x1, self.pot)
minimizer2.set_state(state)
for i in range(10):
minimizer2.one_iteration()
# test that the two minimizers are in the same state
ret1 = self.minimizer.get_result()
ret2 = minimizer2.get_result()
self.assertEqual(ret1.energy, ret2.energy)
self.assertTrue((ret1.coords == ret2.coords).all())
state1 = self.minimizer.get_state()
state2 = minimizer2.get_state()
self.assertTrue((state1.y == state2.y).all())
self.assertTrue((state1.s == state2.s).all())
self.assertTrue((state1.rho == state2.rho).all())
self.assertTrue((state1.dXold == state2.dXold).all())
self.assertTrue((state1.dGold == state2.dGold).all())
self.assertEqual(state1.H0, state2.H0)
self.assertEqual(state1.k, state2.k)
def test_reset(self):
# do several minimization iterations
m1 = LBFGS(self.x, self.pot)
for i in range(10):
m1.one_iteration()
# reset the minimizer and do it again
m1.reset()
e, g = self.pot.getEnergyGradient(self.x)
m1.update_coords(self.x, e, g)
for i in range(10):
m1.one_iteration()
# do the same number of steps of a new minimizer
m2 = LBFGS(self.x, self.pot)
for i in range(10):
m2.one_iteration()
# they should be the same (more or less)
n = min(m1.k, m1.M)
self.assertAlmostEqual(m1.H0, m2.H0, 5)
self.assertEqual(m1.k, m2.k)
arrays_nearly_equal(self, m1.y[:n, :], m2.y[:n, :])
arrays_nearly_equal(self, m1.s[:n, :], m2.s[:n, :])
arrays_nearly_equal(self, m1.rho[:n], m2.rho[:n])
res1 = m1.get_result()
res2 = m2.get_result()
self.assertNotEqual(res1.nfev, res2.nfev)
self.assertNotEqual(res1.nsteps, res2.nsteps)
self.assertAlmostEqual(res1.energy, res2.energy)
arrays_nearly_equal(self, res1.coords, res2.coords)
def setUp(self):
self.system = LJCluster(13)
self.x = self.system.get_random_configuration()
self.pot = self.system.get_potential()
self.minimizer = LBFGS(self.x, self.pot)
def setUp(self):
self.system = LJCluster(13)
self.x = self.system.get_random_configuration()
self.pot = self.system.get_potential()
self.minimizer = LBFGS(self.x, self.pot)
class _TransverseWalker(object):
"""It minimizes the energy in the direction perpendicular to a vector
this class manages the minimization _TransversePotential
Parameters
----------
coords : float array
the starting coordinates
potential : Potential object
eigenvec : float array
energy will be minimized in the direction perpendicular to this vector
energy, gradient : float and float array
the energy and gradient at position coords
minimizer_kwargs : kwargs
these kwargs are passed to the minimizer
"""
def __init__(self,
coords,
potential,
eigenvec,
energy=None,
gradient=None,
**minimizer_kwargs):
self.tspot = _TransversePotential(potential, eigenvec)
if energy is not None and gradient is not None:
transverse_energy, transverse_gradient = self.tspot.projected_energy_gradient(
energy, gradient)
else:
transverse_energy, transverse_gradient = None, None
self.walker = LBFGS(coords,
self.tspot,
energy=transverse_energy,
gradient=transverse_gradient,
**minimizer_kwargs)
def update_eigenvec(self, eigenvec, eigenval):
"""update the vecotr"""
self.tspot.update_vector(eigenvec)
def update_maxstep(self, maxstep):
"""update the maximum step size of the minimizer"""
self.walker.maxstep = float(maxstep)
def update_coords(self, coords, true_energy, true_gradient):
"""update the position of the optimizer
this must be called after update_eigenvec
"""
energy, gradient = self.tspot.projected_energy_gradient(
true_energy, true_gradient)
self.walker.update_coords(coords, energy, gradient)
def stop_criterion_satisfied(self):
"""test if the stop criterion is satisfied"""
return self.walker.stop_criterion_satisfied()
def get_true_energy_gradient(self, coords):
"""return the true energy and gradient"""
return self.tspot.get_true_energy_gradient(coords)
# def get_energy(self):
# """return the true energy
#
# warning it's possible for this to return the wrong energy if the minimizer
# had an aborted line search on the last iteration.
# """
# return self.tspot.true_energy
#
# def get_gradient(self):
# """return the true gradient
#
# warning it's possible for this to return the wrong energy if the minimizer
# had an aborted line search on the last iteration.
# """
# return self.tspot.true_gradient
def get_result(self):
"""return the results object"""
ret = self.walker.get_result()
ret.nfev = self.tspot.nfev
return ret
def run(self, niter):
"""do a specified number of iterations, or until the stop criterion is satisfied"""
for i in range(niter):
if self.stop_criterion_satisfied():
break
self.walker.one_iteration()
return self.get_result()
def test_reset(self):
# do several minimization iterations
m1 = LBFGS(self.x, self.pot)
for i in range(10):
m1.one_iteration()
# reset the minimizer and do it again
m1.reset()
e, g = self.pot.getEnergyGradient(self.x)
m1.update_coords(self.x, e, g)
for i in range(10):
m1.one_iteration()
# do the same number of steps of a new minimizer
m2 = LBFGS(self.x, self.pot)
for i in range(10):
m2.one_iteration()
# they should be the same (more or less)
n = min(m1.k, m1.M)
self.assertAlmostEqual(m1.H0, m2.H0, 5)
self.assertEqual(m1.k, m2.k)
arrays_nearly_equal(self, m1.y[:n, :], m2.y[:n, :])
arrays_nearly_equal(self, m1.s[:n, :], m2.s[:n, :])
arrays_nearly_equal(self, m1.rho[:n], m2.rho[:n])
res1 = m1.get_result()
res2 = m2.get_result()
self.assertNotEqual(res1.nfev, res2.nfev)
self.assertNotEqual(res1.nsteps, res2.nsteps)
self.assertAlmostEqual(res1.energy, res2.energy)
arrays_nearly_equal(self, res1.coords, res2.coords)
class _DimerTranslator(object):
"""object to manage the translation of the dimer using an optimization algorithm
Parameters
----------
coords : float array
the starting point of the dimer
potential : Potential object
eigenvec : float array
the initial direction along which the dimer lies
minimizer_kwargs : kwargs
these kwargs are passed to the optimizer
"""
def __init__(self, coords, potential, eigenvec, **minimizer_kwargs):
self.dimer_potential = _DimerPotential(potential, eigenvec)
self.minimizer = LBFGS(coords, self.dimer_potential,
**minimizer_kwargs)
def stop_criterion_satisfied(self):
"""test if the stop criterion is satisfied"""
return self.minimizer.stop_criterion_satisfied()
def get_true_energy_gradient(self, coords):
"""return the true energy and gradient"""
return self.dimer_potential.get_true_energy_gradient(coords)
# def get_energy(self):
# """return the true energy"""
# return self.dimer_potential.true_energy
#
# def get_gradient(self):
# """return the true gradient"""
# return self.dimer_potential.true_gradient
def update_eigenvec(self, eigenvec, eigenval):
"""update the direction (rotation) of the dimer"""
self.dimer_potential.update_eigenvec(eigenvec)
def update_coords(self, coords, true_energy, true_gradient):
"""update the position of the dimer
this must be called after update_eigenvec
"""
energy, gradient = self.dimer_potential.projected_energy_gradient(
true_energy, true_gradient)
self.minimizer.update_coords(coords, energy, gradient)
def update_maxstep(self, maxstep):
"""change the maximum step size of the optimizer"""
self.minimizer.maxstep = float(maxstep)
def run(self, niter):
"""do a specified number of iterations, or until the stop criterion is satisfied"""
for i in xrange(niter):
if self.stop_criterion_satisfied():
break
self.minimizer.one_iteration()
return self.get_result()
def get_result(self):
"""return the results object"""
return self.minimizer.get_result()
def projected_energy_gradient(self, energy, gradient):
"""return the projected energy and gradient"""
return self.dimer_potential.projected_energy_gradient(energy, gradient)
def reset(self):
LBFGS.reset(self)
self._iter = 0
class TestMYLBFGS_LBFGS(unittest.TestCase):
def setUp(self):
self.setUp1(verbose=False)
def setUp1(self, verbose=False, **kwargs):
np.random.seed(0)
natoms = 18
self.system = LJCluster(natoms)
self.pot = self.system.get_potential()
x = self.system.get_random_configuration()
ret = lbfgs_py(x, self.pot, tol=10)
self.x = ret.coords
self.kwargs = kwargs
self.verbose = verbose
self.M = 4
if self.verbose: iprint = 1
else: iprint = -1
self.myo = MYLBFGS(self.x,
self.pot,
iprint=iprint,
debug=True,
M=self.M)
self.o = LBFGS(self.x,
self.pot,
iprint=iprint,
debug=True,
M=self.M,
**self.kwargs)
def test(self):
N = self.x.size
M = self.M
myo = self.myo
o = self.o
# do one iteration
for i in range(3 * self.M):
myo.one_iteration()
o.one_iteration()
if self.verbose:
print("")
print("H0", myo.H0, o.H0)
print("rho ", o.rho[:])
print("myrho", myo.W[N:N + M])
myret = myo.get_result()
ret = o.get_result()
self.assertAlmostEqual(ret.energy, myret.energy, 4)
self.assertLess(np.max(np.abs(myret.coords - ret.coords)), 1e-6)
# do a second iteration
for i in range(1):
myo.one_iteration()
o.one_iteration()
myret = myo.get_result()
ret = o.get_result()
if self.verbose:
print("H0", myret.H0, ret.H0)
print("rho ", o.rho[:])
print("myrho", myo.W[N:N + M])
self.assertAlmostEqual(ret.energy, myret.energy, 4)
self.assertLess(np.max(np.abs(myret.coords - ret.coords)), 1e-6)
def test_complete(self):
myret = self.myo.run()
ret = self.o.run()
self.assertEqual(ret.nfev, myret.nfev)
self.assertEqual(ret.nsteps, myret.nsteps)
self.assertAlmostEqual(ret.energy, myret.energy, 4)
self.assertLess(np.max(np.abs(myret.coords - ret.coords)), 1e-6)