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Allow Structure.interpolate to extrapolate #3467

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merged 9 commits into from
Nov 29, 2023
Merged

Allow Structure.interpolate to extrapolate #3467

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3d0fb73
added parameter to allow Structure.interpolate to extrapolate beyond …
kyledmiller Nov 10, 2023
efbfe3a
pre-commit auto-fixes
pre-commit-ci[bot] Nov 10, 2023
273dcb5
generalized extrapolation to end_amplitude, a cofactor of the distort…
kyledmiller Nov 29, 2023
9ddb8f8
added tests for new end_amplitude argument in Structure.interpolate()
kyledmiller Nov 29, 2023
492cc82
pre-commit auto-fixes
pre-commit-ci[bot] Nov 29, 2023
cda24c9
fixed too-long comment line
kyledmiller Nov 29, 2023
4b16b74
added note about consistency between start and end structures to docs…
kyledmiller Nov 29, 2023
55af73c
Merge branch 'structure_extrapolate' of github.com:kyledmiller/kdm_py…
kyledmiller Nov 29, 2023
56e0cc4
pre-commit auto-fixes
pre-commit-ci[bot] Nov 29, 2023
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7 changes: 5 additions & 2 deletions pymatgen/core/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2138,6 +2138,7 @@ def interpolate(
interpolate_lattices: bool = False,
pbc: bool = True,
autosort_tol: float = 0,
extrapolation: float = 0,
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Could you add a test for this new keyword?

) -> list[IStructure | Structure]:
"""Interpolate between this structure and end_structure. Useful for
construction of NEB inputs.
Expand All @@ -2157,6 +2158,8 @@ def interpolate(
closest points in this particular structure. This is usually
what you want in a NEB calculation. 0 implies no sorting.
Otherwise, a 0.5 value usually works pretty well.
extrapolation (float): A fractional amount by which to extend the
interpolation beyond the end_structure

Returns:
List of interpolated structures. The starting and ending
Expand Down Expand Up @@ -2212,7 +2215,7 @@ def interpolate(

end_coords = sorted_end_coords

vec = end_coords - start_coords
vec = (1 + extrapolation) * (end_coords - start_coords)
if pbc:
vec[:, self.pbc] -= np.round(vec[:, self.pbc])
sp = self.species_and_occu
Expand All @@ -2222,7 +2225,7 @@ def interpolate(
# interpolate lattice matrices using polar decomposition
# u is a unitary rotation, p is stretch
u, p = polar(np.dot(end_structure.lattice.matrix.T, np.linalg.inv(self.lattice.matrix.T)))
lvec = p - np.identity(3)
lvec = (1 + extrapolation) * (p - np.identity(3))
lstart = self.lattice.matrix.T

for x in images:
Expand Down