From a14cd235faef71f45295f9fae6e2769758d819ea Mon Sep 17 00:00:00 2001 From: csbrasnett Date: Mon, 6 Nov 2023 14:25:52 +0100 Subject: [PATCH] expanded docstring of compute_force_constants --- vermouth/processors/apply_rubber_band.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/vermouth/processors/apply_rubber_band.py b/vermouth/processors/apply_rubber_band.py index f897aae86..100ffc134 100644 --- a/vermouth/processors/apply_rubber_band.py +++ b/vermouth/processors/apply_rubber_band.py @@ -89,6 +89,14 @@ def compute_force_constants(distance_matrix, lower_bound, upper_bound, The force constant can be modified with a decay function, and it can be bounded with a minimum threshold, or a distance upper and lower bonds. + + If decay_factor = decay_power = 0 all forces applied are = base_constant + + Forces applied to distances above upper_bound are removed. + Forces below minimum_force are removed. + + If decay_factor or decay_power != 0, forces below lower_bound are greater + than base_constant, in which case they are set back to = base_constant """ constants = compute_decay(distance_matrix, lower_bound, decay_factor, decay_power) np.fill_diagonal(constants, 0)