Fix issue with complex dimensionality, clean typos and notebooks

pyMBE.py

@@ -464,15 +464,18 @@ def check_dimensionality(self, variable, expected_dimensionality):
         Args:
             `variable`(`pint.Quantity`): Quantity to be checked.
             `expected_dimensionality(`str`): Expected dimension of the variable.
-        """
 
-        try:
-            correct_dimensionality=variable.check(f"[{expected_dimensionality}]")
-        except:
-            raise ValueError(f"The variable {variable} should be a `pint.Quantity` object, instead the variable is {type(variable)}")
-
+        Returns:
+            `bool`: `True` if the variable if of the expected dimensionality, `False` otherwise.
+
+        Note:
+            - `expected_dimensionality` takes dimensionality following the Pint standards [docs](https://pint.readthedocs.io/en/0.10.1/wrapping.html?highlight=dimensionality#checking-dimensionality).
+            - For example, to check for a variable corresponding to a velocity `expected_dimensionality = "[length]/[time]"`    
+        """
+        correct_dimensionality=variable.check(f"{expected_dimensionality}")      
         if not correct_dimensionality:
             raise ValueError(f"The variable {variable} should have a dimensionality of {expected_dimensionality}, instead the variable has a dimensionality of {variable.dimensionality}")
+        return correct_dimensionality
 
     def check_if_df_cell_has_a_value(self, index,key):
         """
@@ -2706,7 +2709,7 @@ def setup_lj_interactions(self, espresso_system, shift_potential=True, combining
         Args:
             espresso_system(`obj`): Instance of a system object from the espressomd library.
             shift_potential(`bool`, optional): If True, a shift will be automatically computed such that the potential is continuous at the cutoff radius. Otherwise, no shift will be applied. Defaults to True.
-            combining_rule(`string`, optional): combining rule used to calculate `sigma` and `epsilon` for the potential betwen a pair of particles. Defaults to 'Lorentz-Berthelot'.
+            combining_rule(`string`, optional): combining rule used to calculate `sigma` and `epsilon` for the potential between a pair of particles. Defaults to 'Lorentz-Berthelot'.
             warning(`bool`, optional): switch to activate/deactivate warning messages. Defaults to True.
 
         Note:
@@ -2749,7 +2752,7 @@ def setup_lj_interactions(self, espresso_system, shift_potential=True, combining
             for ptype in type_pair:
                 for key in lj_parameters_keys:
                     lj_parameters[key].append(self.find_value_from_es_type(es_type=ptype, column_name=key))
-            # If one of the particle has sigma=0, no LJ interations are setuo between that particle type and the others    
+            # If one of the particle has sigma=0, no LJ interations are set up between that particle type and the others    
             if not all([ sigma_value.magnitude for sigma_value in lj_parameters["sigma"]]):
                 continue
             # Apply combining rule

samples/Beyer2024/peptide.py

@@ -70,8 +70,8 @@
     pmb.load_pka_set (filename='parameters/pka_sets/CRC1991.txt')
     model = '2beadAA'  # Model with 2 beads per each aminoacid
     N_peptide_chains = 4
-    sigma_Na=0.35*pmb.units.nm
-    sigma_Cl=0.35*pmb.units.nm
+    sigma_cation=0.35*pmb.units.nm
+    sigma_anion=0.35*pmb.units.nm
     c_salt=1e-2 * pmb.units.mol/ pmb.units.L
     chain_length=len(sequence)*2
 
@@ -81,8 +81,8 @@
     model = '1beadAA'
     N_peptide_chains = 1
     c_salt = 5e-3 * pmb.units.mol/ pmb.units.L
-    sigma_Na=0.2*pmb.units.nm
-    sigma_Cl=0.36*pmb.units.nm
+    sigma_cation=0.2*pmb.units.nm
+    sigma_anion=0.36*pmb.units.nm
     chain_length=len(sequence)
 
 # Simulation parameters
@@ -101,7 +101,9 @@
     raise RuntimeError()
 
 
-pmb.define_peptide (name=sequence, sequence=sequence, model=model)
+pmb.define_peptide (name=sequence, 
+                    sequence=sequence, 
+                    model=model)
 
 # Solution parameters
 cation_name = 'Na'
@@ -110,12 +112,12 @@
 
 pmb.define_particle(name=cation_name,
                     q=1,
-                    sigma=sigma_Na,
+                    sigma=sigma_cation,
                     epsilon=1*pmb.units('reduced_energy'))
 
 pmb.define_particle(name=anion_name,
                     q=-1,
-                    sigma=sigma_Cl,
+                    sigma=sigma_anion,
                     epsilon=1*pmb.units('reduced_energy'))
 
 # System parameters

testsuite/lj_tests.py

@@ -157,7 +157,7 @@
                                 verbose=True)
 print(f"*** Unit test passed ***")
 
-print(f"*** Unit test: test that setup_lj_interactions does not setup any LJ interactions for particles with sigma = 0 ***")
+print(f"*** Unit test: test that setup_lj_interactions does not set up any LJ interactions for particles with sigma = 0 ***")
 
 lj_labels=pmb.filter_df("LennardJones")["name"].values
 # Check that no interaction between particle C and any other particle has been set up