-el fix

vermouth/processors/apply_rubber_band.py

@@ -94,7 +94,9 @@ def compute_force_constants(distance_matrix, lower_bound, upper_bound,
     np.fill_diagonal(constants, 0)
     constants *= base_constant
     constants[constants < minimum_force] = 0
+    constants[constants > base_constant] = 0
     constants[distance_matrix > upper_bound] = 0
+    constants[distance_matrix < lower_bound] = 0    
     return constants
 
 

vermouth/tests/test_apply_rubber_band.py

@@ -537,3 +537,38 @@ 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],
+                                                            [  0,500,500,500]])], # 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
+                          )
+                        )
+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.all() == expected_output.all()