2D PES Generation

2D scans in autodE are available over distances and are optimally parallelised over the available number of cores. For example, to calculate and plot the 2D relaxed surface over the forming C-C distances in a Diels-Alder reaction between ethene and butadiene:

import autode as ade

ade.Config.n_cores = 10  # Distribute over 10 cores

# PES from the current C-C distances (~1.5 Å) to broken (3.0 Å) in 10 steps
pes = ade.pes.RelaxedPESnD(
    species=ade.Molecule("cyclohexene.xyz"),
    rs={(0, 5): (3.0, 10), (3, 4): (3.0, 10)},
)

pes.calculate(method=ade.methods.XTB())
pes.plot("DA_surface.png")
pes.save("DA_surface.npz")

Out:

Surfaces can also be interpolated using a spline. To reload the PES and plot using a 4-fold interpolation (i.e. 10 -> 40 points in each dimension):

import autode as ade

pes = ade.pes.RelaxedPESnD.from_file("DA_surface.npz")
pes.plot("DA_surface_interpolated.png", interp_factor=4)

Out:

where the .xyz file (cyclohexene.xyz) used is:

16
Generated by autodE on: 2021-12-04.
C    -1.25524   0.55843  -0.45127
C    -0.11901   1.52914  -0.34083
C     1.12810   1.05947  -0.22343
C     1.36167  -0.42098  -0.26242
C     0.31173  -1.21999   0.53472
C    -1.08411  -0.56797   0.57151
H    -1.28068   0.12348  -1.46969
H    -2.22404   1.06103  -0.30930
H    -0.31910   2.60539  -0.34475
H     1.98105   1.73907  -0.13515
H     2.37438  -0.67767   0.08526
H     1.32299  -0.74206  -1.32088
H     0.25137  -2.23441   0.11110
H     0.67503  -1.34778   1.56617
H    -1.86306  -1.33147   0.42039
H    -1.26117  -0.13357   1.56876