def test_multi_run():
# NEB
geoms = AnaPot().get_path(10)
cos = NEB(geoms)
neb_kwargs = {
"dump": True,
"h5_group_name": "neb",
}
neb_opt = SteepestDescent(cos, **neb_kwargs)
neb_opt.run()
# GrowingString
geoms = AnaPot().get_path(10)
gsm = GrowingString(geoms, calc_getter=AnaPot, perp_thresh=0.25)
gsm_kwargs = {
"dump": True,
"h5_group_name": "gsm",
"stop_in_when_full": 0,
}
gsm_opt = StringOptimizer(gsm, **gsm_kwargs)
gsm_opt.run()
# calc = geoms[0].calculator
# calc.anim_opt(opt, show=True)
# Simple Optimization
geom = AnaPot().get_path(10)[5]
opt_kwargs = {
"dump": True,
"h5_group_name": "opt",
}
opt = RFOptimizer(geom, **opt_kwargs)
opt.run()
def test_growing_string_climbing(gs_kwargs_, opt_ref_cycle, tsopt_ref_cycle):
calc = AnaPot()
geoms = calc.get_path(num=2)
gs_kwargs = {
"perp_thresh": 0.5,
"reparam_check": "rms",
}
gs_kwargs.update(gs_kwargs_)
cos = GrowingString(geoms, lambda: AnaPot(), **gs_kwargs)
opt_kwargs = {
"gamma_mult": True,
"max_step": 0.04,
"rms_force": 0.1,
"rms_force_only": True,
}
opt = StringOptimizer(cos, **opt_kwargs)
opt.run()
assert opt.is_converged
assert opt.cur_cycle == opt_ref_cycle
# calc = AnaPot()
# calc.anim_opt(opt, show=True)
hei_geom = cos.images[cos.get_hei_index()]
tsopt = RSIRFOptimizer(hei_geom, thresh="gau_vtight")
tsopt.run()
assert tsopt.is_converged
assert tsopt.cur_cycle == tsopt_ref_cycle
def test_neb_springs(neb_kwargs, ref_cycle):
calc = AnaPot()
geoms = calc.get_path(15)
neb = NEB(geoms, **neb_kwargs)
opt = SteepestDescent(neb)
opt.run()
# calc.anim_opt(opt, show=True)
assert (opt.is_converged)
assert (opt.cur_cycle == ref_cycle)
def test_freeend_anapot():
calc = AnaPot()
geoms = calc.get_path(15)
geoms = geoms[3:11]
fe_neb = FreeEndNEB(geoms)
opt = SteepestDescent(fe_neb)
opt.run()
# calc.anim_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == 31
def test_anapot_aneb():
calc = AnaPot()
all_geoms = calc.get_path(10)
aneb = AdaptiveNEB(all_geoms)
opt_kwargs = {
"rms_force": 3e-3,
}
opt = ConjugateGradient(aneb, **opt_kwargs)
opt.run()
# ap = calc.anim_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == 21
def animate(opt):
xlim = (-2, 2.5)
ylim = (0, 5)
levels = (-3, 4, 80)
ap = AnimPlot(AnaPot(), opt, xlim=xlim, ylim=ylim, levels=levels)
ap.animate()
return ap
def get_geoms(coords=None):
if coords is None:
# left = np.array((0.188646, 1.45698, 0))
# right = np.array((0.950829, 1.54153, 0))
left = np.array((0.354902, 1.34229, 0))
right = np.array((0.881002, 1.71074, 0))
right = np.array((0.77, 1.97, 0))
# Very close
# left = np.array((0.531642, 1.41899, 0))
# right = np.array((0.702108, 1.57077, 0))
coords = (right, left)
# near_ts = np.array((0.553726, 1.45458, 0))
# coords = (near_ts, )
# left_far = np.array((-0.455116, 0.926978, 0))
# right_far = np.array((-0.185653, 1.02486, 0))
# coords = (left_far, right_far)
atoms = ("H")
geoms = [Geometry(atoms, c) for c in coords]
for geom in geoms:
geom.set_calculator(AnaPot())
return geoms
def test_anapot_growingstring_opt():
coords = (
(-1.05274, 1.02776, 0),
(1.94101, 3.85427, 0),
)
calc_getter = AnaPot
eps = .05
damp = .05
images = get_geoms(coords, calc_getter)
gs_kwargs = {
"max_nodes": 10,
"perp_thresh": 0.5,
# "perp_thresh": 1,
}
gs = GrowingString(images, calc_getter, reparam_every=1)
# from pysisyphus.optimizers.QuickMin import QuickMin
# opt = QuickMin(gs)
# self.coords = [c.reshape(-1, 3) for c in self.gs.coords_list]
# self.tangents = self.gs.tangent_list
# self.perp_forces = self.gs.perp_force_list
from pysisyphus.optimizers.SteepestDescent import SteepestDescent
# opt = SteepestDescent(gs, alpha=0.05, bt_disable=True, max_cycles=175)
opt = SteepestDescent(gs, alpha=0.05, bt_disable=True, max_cycles=70)
opt.run()
xlim = (-2, 2.5)
ylim = (0, 5)
levels = (-3, 4, 80)
ap = AnimPlot(AnaPot(), opt, xlim=xlim, ylim=ylim, levels=levels)
ap.animate()
def test_optimizers(opt_cls, opt_kwargs_, ref_cycle):
geom = AnaPot.get_geom((0.667, 1.609, 0.))
ref_coords = np.array((1.941, 3.8543, 0.))
opt_kwargs = {
"thresh": "gau_tight",
"dump": False,
"overachieve_factor": 2.,
}
opt_kwargs.update(opt_kwargs_)
opt = opt_cls(geom, **opt_kwargs)
opt.run()
# import matplotlib.pyplot as plt
# calc = geom.calculator
# calc.plot()
# coords = np.array(opt.coords)
# ax = calc.ax
# ax.plot(*coords.T[:2], "ro-")
# plt.show()
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
diff = ref_coords - geom.coords
diff_norm = np.linalg.norm(diff)
print(f"@\tnorm(diff)={diff_norm:.8f}")
assert diff_norm < 6e-5
def test_sqnm():
# geom = AnaPot.get_geom((0, 4, 0))
geom = AnaPot.get_geom((-0.8, 1.73, 0))
opt_kwargs = {
"max_cycles": 15,
"eps": 1e-4,
"E_thresh": 1e-4,
"alpha": 0.5,
"hist_max": 10,
# "thresh": "gau_tight",
"trust_radius": 0.1,
# "bio": False,
"dump": True,
}
opt = StabilizedQNMethod(geom, **opt_kwargs)
# opt = SQNM3(geom, **opt_kwargs)
opt.run()
c = np.array(opt.coords)
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(c[:, 0], c[:, 1], "o-")
plt.show()
def test_dimer(rotation_method, ref_cycle):
coords = (-0.2, 1.1, 0)
geom = Geometry(("X", ), coords)
N_raw = np.array((0.83, 0.27, 0.))
# New implementation
dimer_kwargs = {
"rotation_method": rotation_method,
"calculator": AnaPot(),
"N_raw": N_raw,
"rotation_remove_trans": False,
}
dimer = Dimer(**dimer_kwargs)
geom.set_calculator(dimer)
opt_kwargs = {
"precon": False,
"line_search": None,
"max_step_element": 0.25,
"thresh": "gau_tight",
"max_cycles": 15,
}
opt = PreconLBFGS(geom, **opt_kwargs)
opt.run()
# AnaPot().plot_opt(opt)
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
assert geom.energy == pytest.approx(2.80910484)
def test_dump_neb():
# NEB
geoms = AnaPot().get_path(10)
cos = NEB(geoms)
opt_kwargs = {
"dump": True,
# "rms_force": 1.0,
"h5_group_name": "neb",
}
opt = SteepestDescent(cos, **opt_kwargs)
# opt = SteepestDescent(geoms[7], **opt_kwargs)
opt.run()
# GrowingString
geoms = AnaPot().get_path(10)
gsm = GrowingString(geoms, calc_getter=AnaPot, perp_thresh=0.25)
opt_kwargs = {
"dump": True,
"h5_group_name": "gsm",
"gamma": 10.,
"stop_in_when_full": 0,
}
opt = StringOptimizer(gsm, **opt_kwargs)
opt.run()
calc = geoms[0].calculator
# calc.anim_opt(opt, show=True)
# # Simple Optimization
# geom = AnaPot().get_path(10)[5]
# opt_kwargs = {
# "dump": True,
# "h5_group_name": "opt",
# }
# opt = RFOptimizer(geom, **opt_kwargs)
# opt.run()
return
hei_coords, *_ = cos.get_splined_hei()
ts_geom = geoms[0].copy()
ts_geom.coords = hei_coords
ts_geom.set_calculator(AnaPot())
ts_opt_kwargs = {
# "dump": True,
"thresh": "gau_tight",
}
ts_opt = RSIRFOptimizer(ts_geom, **ts_opt_kwargs)
ts_opt.run()
def run_dimer():
x0 = (-0.5767, 1.6810, 0)
geom0 = AnaPot.get_geom(x0)
N = np.array((-0.9, 0.43, 0))
N /= np.linalg.norm(N)
R = 0.125
coords = dimer_method(geom0, N, R, AnaPot, max_step=0.6, max_cycles=5)
coords = np.array(coords)
pot = AnaPot()
pot.plot()
ax = pot.ax
for i, rot_cycle in enumerate(coords):
ax.plot(*rot_cycle.T[:2], "o-", label=f"Cycle {i:02d}")
ax.legend()
plt.show()
def run_lanczos():
x0 = (-0.5767, 1.6810, 0)
geom0 = AnaPot.get_geom(x0)
w_min, v_min = lanczos(geom0, dx=1e-5)
H = geom0.hessian
w, v = np.linalg.eigh(H)
w_min_ref = w[0]
print(f"w_min_ref={w_min_ref:.6f}")
def test_opt_dump():
geom = AnaPot().get_geom((1, 1, 0.))
calc = geom.calculator
opt_kwargs = {
"dump": True,
}
opt = RFOptimizer(geom, **opt_kwargs)
opt.run()
calc.plot_opt(opt) #, show=True)
def test_conjugate_gradient():
calc = AnaPot()
geoms = calc.get_path(2)
gs_kwargs = {
"perp_thresh": 0.5,
"reparam_check": "rms",
}
gs = GrowingString(geoms, lambda: AnaPot(), **gs_kwargs)
opt_kwargs = {
"keep_last": 0,
"rms_force": 0.02,
"rms_force_only": True,
}
opt = StringOptimizer(gs, **opt_kwargs)
opt.run()
assert opt.is_converged
assert opt.cur_cycle == 23
def test_anapot_lanczos():
geom = AnaPot.get_geom((-0.5767, 1.6810, 0.))
guess = (0.4, 0.3, 0.0)
w_min, v_min = geom_lanczos(geom, guess=guess, dx=1e-5, dl=1e-5, logger=logger)
H = geom.hessian
w, v = np.linalg.eigh(H)
w_ref = w[0]
v_ref = v[:,0]
assert w_min == pytest.approx(w_ref, abs=1e-4)
assert any([np.allclose(v, v_ref, atol=5e-2) for v in (v_min, -v_min)])
def ase_md_playground():
geom = AnaPot.get_geom((0.52, 1.80, 0), atoms=("H", ))
atoms = geom.as_ase_atoms()
# ase_calc = FakeASE(geom.calculator)
# from ase.optimize import BFGS
# dyn = BFGS(atoms)
# dyn.run(fmax=0.05)
import ase
from ase import units
from ase.io.trajectory import Trajectory
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
momenta = atoms.get_momenta()
momenta[0, 2] = 0.
# Zero 3rd dimension
atoms.set_momenta(momenta)
dyn = VelocityVerlet(atoms, .005 * units.fs) # 5 fs time step.
def printenergy(a):
"""Function to print the potential, kinetic and total energy"""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
# Now run the dynamics
printenergy(atoms)
traj_fn = 'asemd.traj'
traj = Trajectory(traj_fn, 'w', atoms)
dyn.attach(traj.write, interval=5)
# dyn.attach(bumms().bimms, interval=1)
dyn.run(10000)
printenergy(atoms)
traj.close()
traj = ase.io.read(traj_fn+"@:")#, "r")
pos = [a.get_positions() for a in traj]
from pysisyphus.constants import BOHR2ANG
pos = np.array(pos) / BOHR2ANG
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*pos[:,0,:2].T)
plt.show()
def test_tshessian_opts(opt_cls, ref_cur_cycle):
geom = AnaPot.get_geom((-0.6, 2.2, 0.))
opt_kwargs = {
"trust_radius": 0.2,
"dump": False,
}
opt = opt_cls(geom, **opt_kwargs)
opt.run()
assert opt.is_converged
assert opt.cur_cycle == ref_cur_cycle
def test_anapot_cbm_rot():
pot = AnaPot()
geoms = (pot.get_geom((0.44, 1.54, 0)), )
N_init = (-0.2, 1, 0)
calc_getter = AnaPot
dimer_kwargs = {
"ana_2dpot": True,
"restrict_step": "max",
"angle_tol": 0.5,
"f_thresh": 1e-4,
"rot_opt": "lbfgs",
"trans_opt": "lbfgs",
"trans_memory": 5,
"f_tran_mod": False,
"N_init": N_init,
"rot_f_thresh": 1e-2,
# "multiple_translations": True,
}
result = dimer_method(geoms, calc_getter, **dimer_kwargs)
true_ts = (0.61173, 1.49297, 0.)
# plot_dimer_cycles(result.dimer_cycles, pot=AnaPot(), true_ts=true_ts[:2])
return result
def test_anapot_irc(irc_cls, mod_kwargs, ref):
geom = AnaPot().get_geom((0.61173, 1.49297, 0.))
kwargs = {
"step_length": 0.1,
"rms_grad_thresh": 1e-2,
}
kwargs.update(**mod_kwargs)
irc = irc_cls(geom, **kwargs)
irc.run()
# geom.calculator.plot_irc(irc, show=True)
assert_anapot_irc(irc)
def run_cos_opt(geoms, between, calc_cls, cos_cls, cos_kwargs, opt_cls,
opt_kwargs):
interpol = Interpolator(geoms, between=between)
images = interpol.interpolate_all()
for image in images:
image.set_calculator(AnaPot())
cos = cos_cls(images, **cos_kwargs)
opt = opt_cls(cos, **opt_kwargs)
opt.run()
return opt
def test_anapot_irc(irc_cls, mod_kwargs, ref):
geom = AnaPot().get_geom((0.61173, 1.49297, 0.))
kwargs = {
"step_length": 0.1,
"rms_grad_thresh": 1e-2,
}
kwargs.update(**mod_kwargs)
irc = irc_cls(geom, **kwargs)
irc.run()
# plot_irc(irc, irc.__class__.__name__)
assert_anapot_irc(irc)
def test_anapot_growing_string(keep_last, ref_cycle):
initial = AnaPot.get_geom((-1.05274, 1.02776, 0))
final = AnaPot.get_geom((1.94101, 3.85427, 0))
geoms = (initial, final)
gs_kwargs = {
"perp_thresh": 0.5,
"reparam_check": "rms",
}
gs = GrowingString(geoms, lambda: AnaPot(), **gs_kwargs)
opt_kwargs = {
# "stop_in_when_full": 3,
"stop_in_when_full": keep_last,
"keep_last": keep_last,
}
opt = StringOptimizer(gs, **opt_kwargs)
opt.run()
# calc = AnaPot()
# calc.anim_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
def test_climb_lanczos():
calc = AnaPot()
geoms = calc.get_path(2)
gs_kwargs = {
"perp_thresh": 0.5,
"reparam_check": "rms",
"climb": True,
"climb_rms": 0.2,
"climb_lanczos": True,
}
gs = GrowingString(geoms, lambda: AnaPot(), **gs_kwargs)
opt_kwargs = {
"keep_last": 0,
"rms_force": 0.02,
"rms_force_only": True,
}
opt = StringOptimizer(gs, **opt_kwargs)
opt.run()
# calc.anim_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == 23
def run_opt(line_search=False, hessian_recalc=None):
geom = AnaPot.get_geom((0.667, 1.609, 0.))
rfo_kwargs = {
"trust_radius": 0.75,
"thresh": "gau_tight",
"hessian_recalc": hessian_recalc,
"line_search": line_search,
# "hessian_init": "calc",
}
rfo = RFOptimizer(geom, **rfo_kwargs)
rfo.run()
conv = rfo.is_converged
cycs = rfo.cur_cycle
return (conv, cycs)
def run_dimer():
x0 = (-0.5767, 1.6810, 0)
geom0 = AnaPot.get_geom(x0)
N = np.array((-0.9, 0.43, 0))
N /= np.linalg.norm(N)
R = 0.125
geom1, geom2 = get_dimer_ends(geom0, N, R, AnaPot)
coords = list()
for i in range(35):
f0 = geom0.forces
norm_f0 = np.linalg.norm(f0)
print(f"{i:0d} {norm_f0:.6f}")
if norm_f0 < 1e-3:
print("Converged!")
break
# Rotation
rot_result = rotate_dimer(geom0, geom1, geom2, N, R)
geom1, geom2, N, C, _ = rot_result
# Translation
trans_result = translate_dimer(geom0, N, C)
update_dimer_ends(geom0, geom1, geom2, N, R)
# Backup for plotting
cs = (geom1.coords, geom0.coords, geom2.coords)
coords.append(cs)
# geom0.calculator.plot_eigenvalue_structure(grid=100)
coords = np.array(coords)
pot = AnaPot()
pot.plot()
ax = pot.ax
for i, rot_cycle in enumerate(coords):
ax.plot(*rot_cycle.T[:2], "o-", label=f"Cycle {i:02d}")
ax.legend()
plt.show()
def test_eulerpc_scipy(scipy_method):
geom = AnaPot().get_geom((0.61173, 1.49297, 0.))
kwargs = {
"step_length": 0.2,
"rms_grad_thresh": 1e-2,
"corr_func": "scipy",
"scipy_method": scipy_method,
}
irc = EulerPC(geom, **kwargs)
irc.run()
# plot_irc(irc, irc.__class__.__name__)
assert_anapot_irc(irc)
def test_add_gaussian():
geom = AnaPot.get_geom((-0.2, 1.1, 0))
N_raw = np.array((0.3, 0.7, 0.))
calc = geom.calculator
dimer_kwargs = {
"calculator": calc,
"N_raw": N_raw,
}
dimer = Dimer(**dimer_kwargs)
geom.set_calculator(dimer)
g0 = dimer.add_gaussian(geom.atoms, geom.coords, dimer.N)
assert g0.height == pytest.approx(0.1708984)
def test_imk(step_length):
geom = AnaPot().get_geom((0.61173, 1.49297, 0.))
irc_kwargs = {
"step_length": step_length,
"rms_grad_thresh": 1e-2,
"corr_first": True,
"corr_first_energy": True,
"corr_bisec_size": 0.0025,
"corr_bisec_energy": True,
}
irc = IMKMod(geom, **irc_kwargs)
irc.run()
# plot_irc(irc, irc.__class__.__name__)
assert_anapot_irc(irc)