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 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_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_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 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 test_fs():
from pysisyphus.calculators.XTB import XTB
from pysisyphus.cos.FreezingString import FreezingString
# educt = geom_from_library("ciscis_24hexadiene_xtbopt.xyz")
# product = geom_from_library("trans34dimethylcyclobutene.xyz")
educt = AnaPot.get_geom((-1.05274, 1.02776, 0))
product = AnaPot.get_geom((1.94101, 3.85427, 0))
images = (educt, product)
def calc_getter():
return AnaPot()
fs = FreezingString(images, calc_getter, max_nodes=10)
from pysisyphus.optimizers.SteepestDescent import SteepestDescent
sd = SteepestDescent(fs)
sd.run()
pot = AnaPot()
pot.plot()
crds = fs.allcoords.reshape(-1, 3)
# pot.ax.plot(c[:,0], c[:,1], "o-")
pot.ax.plot(*crds[:,:2].T, "o-")
plt.show()
from pysisyphus.optimizers.StringOptimizer import StringOptimizer
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 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 test_line_search(line_search, ref_cycle, ref_energy):
geom = AnaPot.get_geom((0.687, 1.57, 0.))
opt_kwargs = {
"thresh": "gau_tight",
"line_search": line_search,
"max_cycles": 64,
"precon": False,
}
opt = PreconSteepestDescent(geom, **opt_kwargs)
opt.run()
# geom.calculator.plot_opt(opt)
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
assert geom.energy == pytest.approx(ref_energy)
def test_line_search(line_search, ref_cycle):
geom = AnaPot.get_geom((0.687, 1.57, 0.0))
opt_kwargs = {
"thresh": "gau_tight",
"line_search": line_search,
"max_cycles": 64,
"precon": False,
}
opt = PreconLBFGS(geom, **opt_kwargs)
opt.run()
# geom.calculator.plot_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
assert geom.energy == pytest.approx(0.98555442)
def test_armijo(line_search, ref_cycle):
geom = AnaPot.get_geom((0.2, 1.3, 0.0))
opt_kwargs = {
"thresh": "gau_tight",
"precon": False,
# "use_grad": use_grad,
"line_search": line_search,
}
opt = PreconLBFGS(geom, **opt_kwargs)
opt.run()
# geom.calculator.plot_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == ref_cycle
assert geom.energy == pytest.approx(-0.51340926)
def test_diis():
geom = AnaPot.get_geom((0.4333, 3.14286, 0.))
opt_kwargs = {
# "max_step": 0.5,
# "trust_max": 0.1,
"thresh": "gau_tight",
# "eins": True,
"zwei": True,
}
opt = RFOptimizer(geom, **opt_kwargs)
opt.run()
calc = geom.calculator
calc.plot()
ax = calc.ax
cs = np.array(opt.coords)
ax.plot(*cs.T[:2], "ro-")
plt.show()
def test_pred():
geom = AnaPot.get_geom((-0.174, 1.27, 0.))
calc = geom.calculator
trst = 0.05
opt_kwargs = {
"trust_min": trst,
"trust_radius": trst,
"trust_max": 0.3,
"hessian_recalc": 1,
"max_micro_cycles": 1,
}
opt = RSPRFOptimizer(geom, **opt_kwargs)
opt.run()
coords = np.array(opt.coords)
calc.plot()
ax = calc.ax
ax.plot(*coords.T[:2], "ro-")
plt.show()
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_linesearch():
geom = AnaPot.get_geom((0.667, 1.609, 0.))
rfo_kwargs = {
# "trust_radius": 0.75,
"trust_radius": 0.75,
"thresh": "gau_tight",
# "max_cycles": 14,
# "hessian_recalc": 3,
# "hessian_init": "calc",
"line_search": True,
}
rfo = RFOptimizer(geom, **rfo_kwargs)
rfo.run()
coords = np.array(rfo.coords)
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*coords.T[:2], "o-")
for i, coords in enumerate(coords):
ax.annotate(f"{i}", coords[:2])
plt.show()
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_velocity_verlet():
geom = AnaPot.get_geom((0.52, 1.80, 0))
x0 = geom.coords.copy()
v0 = .1 * np.random.rand(*geom.coords.shape)
t = 3
dts = (.005, .01, .02, .04, .08)
all_xs = list()
for dt in dts:
geom.coords = x0.copy()
md_kwargs = {
"v0": v0.copy(),
"t": t,
"dt": dt,
}
md_result = md(geom, **md_kwargs)
all_xs.append(md_result.coords)
calc = geom.calculator
calc.plot()
ax = calc.ax
for dt, xs in zip(dts, all_xs):
ax.plot(*xs.T[:2], "o-", label=f"dt={dt:.3f}")
# ax.plot(*xs.T[:2], "-", label=f"dt={dt:.3f}")
ax.legend()
plt.show()
def test_sd_gediis():
geom = AnaPot.get_geom((0.4333, 3.14286, 0.))
trust = 0.3
H = np.eye(geom.coords.size)
ens = list()
cs = list()
dcs = list()
fs = list()
pairs = list()
for i in range(25):
forces = geom.forces
energy = geom.energy
cs.append(geom.coords)
fs.append(forces)
ens.append(energy)
forces_norm = np.linalg.norm(forces)
print(f"{i:02d}: {forces_norm:.6f}")
if forces_norm < 1e-3:
print("Converged!")
break
# Calculate reference step
step = get_step(H, forces, trust)
if len(fs) > 1:
gediis_res = gediis(cs, ens, fs)
if gediis_res is not None:
# Inter-/extrapolate coordinates and forces
coords_ = gediis_res.coords
forces = gediis_res.forces
dcs.append(coords_)
geom.coords = coords_
forces_norm = np.linalg.norm(forces)
# Get new step from GEDIIS coordinates & forces
step = get_step(H, forces, trust)
new_coords = geom.coords + step
geom.coords = new_coords
cs = np.array(cs)
dcs = np.array(dcs)
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*cs.T[:2], "o-")
for i, cs_ in enumerate(cs):
ax.annotate(f"{i:02d}", cs_[:2])
ax.plot(*dcs.T[:2], "o-")
for oc, dc, rs in pairs:
line = mlines.Line2D((oc[0], dc[0]), (oc[1], dc[1]),
ls="--",
color="k")
ax.add_artist(line)
line = mlines.Line2D((oc[0], rs[0]), (oc[1], rs[1]),
ls="--",
color="r")
ax.add_artist(line)
plt.show()
def run():
geom = AnaPot.get_geom((-1, 3, 0))
print(geom)
def prep_post(geom):
return {
"coords": geom.coords.tolist(),
"gradient": geom.gradient.tolist(),
"energy": float(geom.energy),
}
req_kwargs = {
"headers": {
"Content-type": "application/json",
},
}
base_url = "http://localhost:8080/"
def send_json(path, data):
url = base_url + path
response = requests.post(url=url, data=json.dumps(data), **req_kwargs)
return response
init = {
"key": "cg",
"alpha": 0.1,
"gdiis": False,
"line_search": False,
}
init_resp = send_json("init", init)
print("Init response", init_resp)
coords = list()
opt_state = OptState(alpha=0.3, key="cg")
for i in range(50):
coords.append(geom.coords)
print("\tcur. coords", geom.coords)
gradient = geom.gradient
norm = np.linalg.norm(gradient)
print(f"{i:02d}: norm(grad)={norm:.6f}")
if norm <= 0.1:
print("Converged")
break
pp = prep_post(geom)
# # resp = requests.post(**req_kwargs, data=pp)
# resp = send_json("step", pp)
# resp_data = resp.json()
# step = resp_data["step"]
# status = resp_data["status"]
step, status = opt_state.step(geom.coords, geom.energy, geom.gradient)
new_coords = geom.coords + step
# print("\t", status)
geom.coords = new_coords
print()
print()
# import pdb; pdb.set_trace()
# pass
coords = np.array(coords)
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*coords.T[:2], "ro-")
for i, xy in enumerate(coords[:, :2]):
ax.annotate(str(i), xy)
plt.show()
def get_geoms():
initial = AnaPot.get_geom((-1.05274, 1.02776, 0))
final = AnaPot.get_geom((1.94101, 3.85427, 0))
geoms = (initial, final)
return geoms
def test_sd_gdiis():
geom = AnaPot.get_geom((0.4333, 3.14286, 0.))
trust = 0.3
H = np.eye(geom.coords.size)
cs = list()
dcs = list()
fs = list()
pairs = list()
for i in range(50):
forces = geom.forces
cs.append(geom.coords)
fs.append(forces)
forces_norm = np.linalg.norm(forces)
print(f"{i:02d}: {forces_norm:.6f}")
if forces_norm < 1e-3:
print("Converged!")
break
# Calculate reference step
step = get_step(H, forces, trust)
if len(fs) > 1:
gdiis_kwargs = {
"coords": cs,
"forces": fs,
"ref_step": step,
}
res = gdiis(fs, **gdiis_kwargs)
if res:
# Inter-/extrapolate coordinates and forces
coords_ = res.coords
forces = res.forces
dcs.append(coords_)
pairs.append((geom.coords.copy(), coords_, geom.coords + step))
geom.coords = coords_
forces_norm = np.linalg.norm(forces)
# Get new step from DIIS coordinates & forces
step = get_step(H, forces, trust)
new_coords = geom.coords + step
geom.coords = new_coords
# return
cs = np.array(cs)
dcs = np.array(dcs)
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*cs.T[:2], "o-")
for i, cs_ in enumerate(cs):
ax.annotate(f"{i:02d}", cs_[:2])
ax.plot(*dcs.T[:2], "o-")
for oc, dc, rs in pairs:
line = mlines.Line2D((oc[0], dc[0]), (oc[1], dc[1]),
ls="--",
color="k")
ax.add_artist(line)
line = mlines.Line2D((oc[0], rs[0]), (oc[1], rs[1]),
ls="--",
color="r")
ax.add_artist(line)
plt.show()
def test_dwi():
dwi = DWI()
coords = np.array((
(-0.222, 1.413, 0.),
(-0.812, 1.242, 0.),
))
geom = AnaPot.get_geom(coords[0])
calc = geom.calculator
c1 = geom.coords
e1 = geom.energy
g1 = geom.gradient
h1 = geom.hessian
dwi.update(c1, e1, g1, h1)
geom.coords = coords[1]
c2 = geom.coords
e2 = geom.energy
g2 = geom.gradient
h2 = geom.hessian
dwi.update(c2, e2, g2, h2)
points = 10
step = (coords[1] - coords[0]) / (points - 1)
true_ens = list()
true_grads = list()
interpol_ens = list()
interpol_grads = list()
findiff = 1e-4
fd_grads = list()
for i in range(points):
new_coords = coords[0] + i * step
geom.coords = new_coords
true_grad = geom.gradient
true_grads.append(true_grad)
true_energy = geom.energy
true_ens.append(true_energy)
interpol_energy, interpol_grad = dwi.interpolate(new_coords,
gradient=True)
interpol_ens.append(interpol_energy)
interpol_grads.append(interpol_grad)
fd_grad = list()
for i in range(3):
fd_step = np.zeros(3)
fd_step[i] = findiff
plus_val = dwi.interpolate(new_coords + fd_step)
minus_val = dwi.interpolate(new_coords - fd_step)
fd = (plus_val - minus_val) / (2 * findiff)
fd_grad.append(fd)
fd_grads.append(fd_grad)
true_ens = np.array(true_ens)
interpol_ens = np.array(interpol_ens)
true_grads = np.array(true_grads)
interpol_grads = np.array(interpol_grads)
fd_grads = np.array(fd_grads)
np.testing.assert_allclose(interpol_grads, fd_grads)
quiver_xs = np.arange(interpol_ens.size)
quiver_true_ys = true_ens
quiver_interpol_ys = interpol_ens
fig, ax = plt.subplots()
ax.plot(true_ens, label="True")
ax.plot(interpol_ens, label="DWI")
tg_U = true_grads[:, 0]
tg_V = true_grads[:, 1]
ti_U = interpol_grads[:, 0]
ti_V = interpol_grads[:, 1]
ax.quiver(quiver_xs,
quiver_true_ys,
tg_U,
tg_V,
color="b",
label="grad(True)")
ax.quiver(quiver_xs,
quiver_interpol_ys,
ti_U,
ti_V,
color="orange",
label="grad(DWI)")
ax.legend()
plt.show()
def test_euler():
dwi = DWI()
coords = np.array((
(-0.222, 1.413, 0.),
(-0.812, 1.242, 0.),
))
# Half step
# diff = coords[1] - coords[0]
# coords[1] = coords[0] + 0.5*diff
geom = AnaPot.get_geom(coords[0])
calc = geom.calculator
c1 = geom.coords
e1 = geom.energy
g1 = geom.gradient
h1 = geom.hessian
dwi.update(c1, e1, g1, h1)
geom.coords = coords[1]
c2 = geom.coords
e2 = geom.energy
g2 = geom.gradient
h2 = geom.hessian
dwi.update(c2, e2, g2, h2)
# Euler integration
norm = np.linalg.norm(coords[1] - coords[0])
print(f" norm={norm:.8f}")
all_coords = list()
richardson = dict()
errors = list()
for k in range(10):
points = 10 * (2**k) + 1
corr_step_length = norm / (points - 1)
# print("corr_step_length", corr_step_length)
cur_coords = coords[0].copy()
k_coords = list()
length = 0
while True:
k_coords.append(cur_coords.copy())
if length >= norm:
# print(f"Converged! length={length:.8f}, length-step={length-corr_step_length:.8f}")
print(f"Converged! length={length:.8f}")
break
energy, gradient = dwi.interpolate(cur_coords, gradient=True)
cur_coords += corr_step_length * -gradient / np.linalg.norm(
gradient)
length += corr_step_length
# Check for oscillation
try:
prev_coords = k_coords[-2]
osc_norm = np.linalg.norm(cur_coords - prev_coords)
if osc_norm <= corr_step_length:
print("Detected oscillation. Breaking!")
# TODO: handle this by restarting everyhting with a smaller stepsize.
# Check 10.1039/c7cp03722h SI
assert False, "This case is not yet handled"
break
except IndexError:
pass
richardson[(k, 0)] = cur_coords
# Refine using Richardson extrapolation
# Set additional values using Richard extrapolation
for j in range(1, k + 1):
print(f"k={k},j={j}")
richardson[(k, j)] = ((2**j) * richardson[(k, j-1)] - richardson[(k-1, j-1)]) \
/ (2**j-1)
if k > 0:
# RMS of coordinates
error = np.sqrt(
np.mean((richardson[(k, k)] - richardson[(k - 1, k - 1)])**2))
print(f"\terror={error:.8e}")
errors.append(error)
if error <= 1e-6:
break
all_coords.append(np.array(k_coords))
print("Richardson table")
pprint(richardson)
print()
print("Errors")
erros = np.array(errors)
print(errors)
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*coords.T[:2], "r-")
for i, ac in enumerate(all_coords, 1):
ax.plot(*ac.T[:2], label=i)
ax.legend()
plt.show()
def test_bias_translation():
# coords = (-1.05, 1.02, 0)
coords = (-1.009, 1.024, 0)
geom = AnaPot.get_geom(coords)
N_raw = np.array((0.9603, 0.2789, 0.))
calc = geom.calculator
# calc.plot_eigenvalue_structure()
dimer_kwargs = {
"calculator": calc,
"N_raw": N_raw,
"rotation_disable": True,
# "rotation_method": "direct",
# "bias_rotation": True,
"bias_translation": True,
# "bias_gaussian_dot": 0.5,
}
dimer = Dimer(**dimer_kwargs)
geom.set_calculator(dimer)
import matplotlib.pyplot as plt
def plot(dimer, coords0, title=None, step_norms=None):
if step_norms is None:
step_norms = list()
step_norms_max = 0.5
else:
step_norms_max = max(step_norms)
N = dimer.N
# steps = np.linspace(-0.025, 0.125, 30)
steps = np.linspace(-0.05, max(step_norms_max, 0.1), 50)
stepsN = steps[:, None] * N
Ncoords = coords0 + steps[:, None] * N
results = [dimer.get_forces(geom.atoms, coords) for coords in Ncoords]
ens, forces = zip(*[(r["energy"], r["forces"]) for r in results])
forces = np.array(forces)
norms = np.linalg.norm(forces, axis=1)
step1_norm = np.linalg.norm(
np.array((-0.759042, 1.09659, 0.) - coords0))
# fig, (ax0, ax1) = plt.subplots(nrows=2)
fig, (ax0, ax1, ax2) = plt.subplots(nrows=3)
ax0.plot(steps, ens)
ax0.set_title("energy")
ax1.plot(steps, norms, "o-")
ax1.set_title("norm(forces)")
# ax2.plot(*forces.T[:2], "o-")
# for i, f in enumerate(forces):
# ax2.annotate(i, f[:2])
# ax2.quiver(Ncoords.[::2]
# ax2.quiver(Ncoords[:,0], Ncoords[:,1], forces[:,0], forces[:,1])
ax2.quiver(stepsN[:, 0],
stepsN[:, 1],
forces[:, 0],
forces[:, 1],
scale=10)
ax2.axvline(0.0529)
for ax in (ax0, ax1):
ax.axvline(0, color="r", ls="--")
for i, x in enumerate(step_norms):
for ax in (ax0, ax1):
ax.axvline(x, color="k", ls="--")
mi, ma = ax.get_ylim()
y = (mi + ma) / 2
ax.annotate(i, (x, y))
if title:
fig.suptitle(title)
return fig
coords0 = geom.coords.copy()
# f_ub = plot(dimer, coords0, "unbiased")
g0 = dimer.add_gaussian(geom.atoms, geom.coords, dimer.N)
print(g0)
# f_b = plot(dimer, coords0, "biased")
plt.show()
# return
opt_kwargs = {
"precon": False,
# "max_step_element": 0.06,
# "max_step_element": 0.03,
"max_step_element": 0.0529,
# "max_cycles": 9,
"max_cycles": 10,
"dump": True,
}
# opt = PreconLBFGS(geom, **opt_kwargs)
from pysisyphus.optimizers.PreconSteepestDescent import PreconSteepestDescent
opt = PreconSteepestDescent(geom, **opt_kwargs)
opt.run()
step_norms = np.linalg.norm([c - coords0 for c in opt.coords], axis=1)
f_b = plot(dimer, coords0, "biased", step_norms)
print(step_norms)
for i, step in enumerate(opt.steps):
print(i, step)
# calc.plot_opt(opt)
plt.show()