diff --git a/src/core/reaction_ensemble.cpp b/src/core/reaction_ensemble.cpp index f36232674ab..ec63e5ac772 100644 --- a/src/core/reaction_ensemble.cpp +++ b/src/core/reaction_ensemble.cpp @@ -58,7 +58,7 @@ double average_list_of_allowed_entries(const std::vector &vector) { } /** - * Checks whether a number is in a std:vector of numbers. + * Checks whether a number is in a std::vector of numbers. */ template bool is_in_list(T value, const std::vector &list) { for (int i = 0; i < list.size(); i++) { diff --git a/src/core/reaction_ensemble.hpp b/src/core/reaction_ensemble.hpp index 3b9095a8a8a..c9f50dae8bd 100644 --- a/src/core/reaction_ensemble.hpp +++ b/src/core/reaction_ensemble.hpp @@ -224,8 +224,7 @@ class ReactionAlgorithm { get_random_position_in_box_enhanced_proposal_of_small_radii(); }; -////////////////////////////////////////////////////////////////actual -/// declaration of specific reaction algorithms +///////////////////////////// actual declaration of specific reaction algorithms /** Reaction ensemble method according to smith94x. * Works for the reaction ensemble at constant volume and temperature. For the diff --git a/src/python/espressomd/reaction_ensemble.pyx b/src/python/espressomd/reaction_ensemble.pyx index 01219a75329..6eb1bafbc95 100644 --- a/src/python/espressomd/reaction_ensemble.pyx +++ b/src/python/espressomd/reaction_ensemble.pyx @@ -32,7 +32,7 @@ cdef class ReactionAlgorithm: be inserted. This is useful to avoid integrator failures if particles are too close and there is a diverging repulsive interaction, or to prevent two oppositely charged particles from being placed on top of - each other. The Boltzmann factor :math:`\exp(-\\beta E)` gives these + each other. The Boltzmann factor :math:`\\exp(-\\beta E)` gives these configurations a small contribution to the partition function, therefore they can be neglected. """ @@ -157,21 +157,21 @@ cdef class ReactionAlgorithm: Parameters ---------- gamma : :obj:`float` - Equilibrium constant of the reaction, :math:`\gamma` (see the User + Equilibrium constant of the reaction, :math:`\\gamma` (see the User guide, section 6.6 for the definition and further details). reactant_types : list of :obj:`int` List of particle types of reactants in the reaction. - reactant_coefficients : list + reactant_coefficients : list of :obj:`int` List of stoichiometric coefficients of the reactants in the same order as the list of their types. - product_types : list + product_types : list of :obj:`int` List of particle types of products in the reaction. - product_coefficients : list + product_coefficients : list of :obj:`int` List of stoichiometric coefficients of products of the reaction in the same order as the list of their types default_charges : dictionary A dictionary of default charges for types that occur in the provided reaction. - check_for_electroneutrality : Boolean + check_for_electroneutrality : :obj:`bool` Check for electroneutrality of the given reaction if True. """ @@ -356,7 +356,7 @@ cdef class ReactionEnsemble(ReactionAlgorithm): if k in self._valid_keys(): self._params[k] = kwargs[k] else: - raise KeyError("%s is not a vaild key" % k) + raise KeyError("%s is not a valid key" % k) self._set_params_in_es_core() @@ -379,7 +379,7 @@ cdef class ConstantpHEnsemble(ReactionAlgorithm): if k in self._valid_keys(): self._params[k] = kwargs[k] else: - raise KeyError("%s is not a vaild key" % k) + raise KeyError("%s is not a valid key" % k) self._set_params_in_es_core() @@ -425,7 +425,7 @@ cdef class WangLandauReactionEnsemble(ReactionAlgorithm): if k in self._valid_keys(): self._params[k] = kwargs[k] else: - raise KeyError("%s is not a vaild key" % k) + raise KeyError("%s is not a valid key" % k) self.WLRptr.reset(new CWangLandauReactionEnsemble(int(self._params["seed"]))) self.RE = self.WLRptr.get() @@ -435,8 +435,8 @@ cdef class WangLandauReactionEnsemble(ReactionAlgorithm): def reaction(self, reaction_steps=1): """ Performs reaction_steps reactions. Sets the number of reaction steps - which are performed at once. Do not use too many reaction steps steps - consecutively without having conformation changing steps in between + which are performed at once. Do not use too many reaction steps + consecutively without having conformation-changing steps in-between (especially important for the Wang-Landau reaction ensemble). Providing a number for the parameter reaction steps reduces the need for the interpreter to be called between consecutive reactions. @@ -461,7 +461,7 @@ cdef class WangLandauReactionEnsemble(ReactionAlgorithm): Minimum value of the collective variable. max : :obj:`float` Maximum value of the collective variable. - corresponding_acid_types : list + corresponding_acid_types : list of :obj:`int` List of the types of the version of the species. """ @@ -547,7 +547,7 @@ cdef class WangLandauReactionEnsemble(ReactionAlgorithm): ---------- final_wang_landau_parameter : :obj:`float` Sets the final Wang-Landau parameter, which is the Wang-Landau - parameter after which the simulation should stop.). + parameter after which the simulation should stop. full_path_to_output_filename : :obj:`str` Sets the path to the output file of the Wang-Landau algorithm which contains the Wang-Landau potential @@ -598,9 +598,9 @@ cdef class WangLandauReactionEnsemble(ReactionAlgorithm): Records the minimum and maximum potential energy as a function of the degree of association in a preliminary Wang-Landau reaction ensemble simulation where the acceptance probability includes the factor - :math:`\exp(-\\beta \\Delta E_{pot})`. The minimal and maximal + :math:`\\exp(-\\beta \\Delta E_{pot})`. The minimal and maximal potential energies which occur in the system are needed for the energy - reweighting simulations where the factor :math:`\exp(-\\beta \\Delta E_{pot})` + reweighting simulations where the factor :math:`\\exp(-\\beta \\Delta E_{pot})` is not included in the acceptance probability in order to avoid choosing the wrong potential energy boundaries. @@ -689,7 +689,7 @@ cdef class WidomInsertion(ReactionAlgorithm): if k in self._valid_keys(): self._params[k] = kwargs[k] else: - raise KeyError("%s is not a vaild key" % k) + raise KeyError("%s is not a valid key" % k) self._set_params_in_es_core()