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_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_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
