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GoodrichGroup
common_utils
Commits
e658fc77
Commit
e658fc77
authored
Jun 08, 2022
by
Andreas EHRMANN
Browse files
Update common_utils/dneb.py
parent
b4d53ed8
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1
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common_utils/dneb.py
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e658fc77
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@@ -183,8 +183,8 @@ def setup_endpoint_minimization(energy_fn,
""" Independently minimize a collection of systems. In practice this will
be DNEB endpoints.
Args:
Rs: array of initial positions of shape (n, N, d
imension
), where n is number of
systems, N is the system size, and d
imension
is the dimension of space.
Rs: array of initial positions of shape (n, N, d), where n is number of
systems, N is the system size, and d is the dimension of space.
Return:
- array of final positions with the same shape.
- maxgrad
...
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@@ -288,7 +288,7 @@ def find_DNEB_paths(R_endpoints,
This is the primary API function.
Args:
R_endpoints: array of shape (e, N, d
imension
) corresponding to e endpoints
R_endpoints: array of shape (e, N, d) corresponding to e endpoints
transitions: array of shape (t, 2) where t is the number of transitions to consider.
If e==2, set transitions to [[0,1]] since there is only 1 possible transition.
true_energy_fn: A function that takes an (N,d) array of positions and
...
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@@ -299,7 +299,7 @@ def find_DNEB_paths(R_endpoints,
Returns:
- array of shape (e, N, d
imension
) corresponding to the minimized endpoints
- array of shape (e, N, d) corresponding to the minimized endpoints
- list of length t containing DNEB results
"""
...
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