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-el fix #559

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merged 8 commits into from
Nov 13, 2023
Merged

-el fix #559

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d0feb7f
ensured el flag is used
csbrasnett Oct 31, 2023
8ef0e42
fixed el threshold application
csbrasnett Oct 31, 2023
edbfb6f
removed brackets
csbrasnett Oct 31, 2023
bcf4699
didn't account for constant forces
csbrasnett Oct 31, 2023
99c0452
added tests for rubber band application
csbrasnett Nov 1, 2023
9104cec
added decay tests
csbrasnett Nov 1, 2023
1617e84
corrected behaviour
csbrasnett Nov 3, 2023
a14cd23
expanded docstring of compute_force_constants
csbrasnett Nov 6, 2023
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9 changes: 9 additions & 0 deletions vermouth/processors/apply_rubber_band.py
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Expand Up @@ -89,11 +89,20 @@ 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)
constants *= base_constant
constants[constants < minimum_force] = 0
constants[constants > base_constant] = base_constant
constants[distance_matrix > upper_bound] = 0
return constants

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47 changes: 47 additions & 0 deletions vermouth/tests/test_apply_rubber_band.py
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Expand Up @@ -537,3 +537,50 @@ def test_bail_out_on_nan(caplog, test_molecule):
assert record.getMessage() == required_warning
assert len(caplog.records) == 1
assert test_molecule.interactions['bonds'] == []


@pytest.mark.parametrize('lower_bound, upper_bound, decay_factor, decay_power, base_constant, minimum_force, expected_output',
([1, 2, 0, 0, 500, 400, np.array([[ 0,500,500, 0],
[500, 0,500,500],
[500,500, 0,500],
[ 0,500,500, 0]])], # no decays, return the base constant within the bounds
[1, 2, 0, 0, 500, 600, np.array([[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]])], # all forces less than the minumum force
[1, 0.5, 0, 0, 500, 600, np.array([[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]])], # all distances larger than the upper bound
[4, 2, 0, 0, 500, 600, np.array([[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]])], # all distances less than the lower bound
[1, 3, 0.1, 0, 500, 400, np.array([[ 0. , 452.41870902, 452.41870902, 452.41870902],
[452.41870902, 0. , 452.41870902, 452.41870902],
[452.41870902, 452.41870902, 0. , 452.41870902],
[452.41870902, 452.41870902, 452.41870902, 0. ]])], # with a decay factor
[1, 3, 0, 2, 500, 400, np.array([[ 0,500,500,500],
[500, 0,500,500],
[500,500, 0,500],
[500,500,500, 0]])], # with a decay factor
[1, 3, 0.1, 2, 500, 400, np.array([[ 0. , 500. , 452.41870902, 0. ],
[500. , 0. , 500. , 452.41870902],
[452.41870902, 500. , 0. , 500. ],
[ 0. , 452.41870902, 500. , 0. ]])], # with a complex decay
)
)
def test_compute_force_constants(lower_bound, upper_bound, decay_factor, decay_power, base_constant, minimum_force, expected_output):
# Define the constant distance_matrix for the test cases
distance_matrix = np.array([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]])

# Call the compute_force_constants function with the constant distance_matrix and varied parameters
result = vermouth.processors.apply_rubber_band.compute_force_constants(distance_matrix, lower_bound, upper_bound,
decay_factor, decay_power, base_constant,
minimum_force)

# Assert the result against the expected output
assert result == pytest.approx(expected_output)