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expanded docstring of compute_force_constants
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csbrasnett committed Nov 6, 2023
1 parent 1617e84 commit a14cd23
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8 changes: 8 additions & 0 deletions vermouth/processors/apply_rubber_band.py
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Expand Up @@ -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)
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