4.3 Software Capabilities
61
The upper part of VISO also contains a number of datatype properties, mostly
Boolean ones (e.g. viso:is_free, viso:has_a_gpu_version), but not only
(e.g. viso:has_main_name, viso:has_version_identifier) to characterize the software
[32].
Below viso:general, the EL, AM and CO branches of VISO expand on the categories viso:model_feature, viso:solver_feature and viso:model_type (cf. Fig. 4.2 for
the AM one). These classes are the richest ones of VISO, and they contain most
of the concepts that are peculiar to our domain. The three branches have a common structure, in that the subclasses of viso:model_feature are further classified into
(non-disjoint) classes of viso:materials_relation_trait, viso:physical_equation_trait
and viso:external_condition_trait. For clarity, we systematically use trait here, and not
aspect, since the latter keyword has a different and well-defined role within OSMO
and MODA.
In the last part of this section, we look into more detail at the viso-am branch, which
was designed considering Molecular Dynamics, Molecular Mechanics, Dissipative
Particle Dynamics and Monte Carlo methods. First of all, our choice to treat together
the atomistic and mesoscopic models is motivated by the fact that in many cases
they rely on the same numerical methods and a given software tool can address
both. Also, the meaning of “mesoscopic” within RoMM is different from the usual
acceptation: as soon as two or more atoms are grouped into an entity, this is considered
a mesoscopic model; since united-atom models already fall into this class, treating
these two granularity levels jointly seems well justified.
It is important to underline that the RoMM [30] classification principle is based
on what a modelling entity represents , a criterion that is indeed well suited to multiscale modelling. A complementary and quite natural classification could be based on
the mathematical nature of the modelling entity: for example, the classical models
could be distinguished in particle-based and field-based ones. While as a rule of
thumb AM models are particle-based and CO models are field-based, typically there
are also fields in AM models, discrete particles in CO and classical particles in EL
ones. Above all, it is important to realize that the two classifications are fundamentally
different: to give an extreme example, we could have a particle-based model of the
solar system, where each particle represents a planet!
In this direction, an important concept in VISO is that of viso:model_object
5
(cf. Fig. 4.2) which is the type of object entering the model and carrying degrees
of freedom. To be able to encompass different chemical objects, we need to adopt
a neutral vocabulary; in the AM branch, we choose to use viso-am:interaction_site
to indicate a point which is involved in (experiences) some interaction; it can represent the centre of a physical particle (an atom, a coarse-grained bead), but also be
a fictitious particle. Similarly, a viso-am:connected_object, where connectedness is
via bonds of some type, could be a molecule (in the chemical sense) or an aggregate. Finally, we have viso-am:interaction_surface, which is a surface affecting the
interactions and is treated as continuum, not as a collection of sites; for example, it
could be a wall. It is clear that our approach focuses on the mathematical nature of
5 Not to be confused with the “Object model” concept of Chap. 2.
61
The upper part of VISO also contains a number of datatype properties, mostly
Boolean ones (e.g. viso:is_free, viso:has_a_gpu_version), but not only
(e.g. viso:has_main_name, viso:has_version_identifier) to characterize the software
[32].
Below viso:general, the EL, AM and CO branches of VISO expand on the categories viso:model_feature, viso:solver_feature and viso:model_type (cf. Fig. 4.2 for
the AM one). These classes are the richest ones of VISO, and they contain most
of the concepts that are peculiar to our domain. The three branches have a common structure, in that the subclasses of viso:model_feature are further classified into
(non-disjoint) classes of viso:materials_relation_trait, viso:physical_equation_trait
and viso:external_condition_trait. For clarity, we systematically use trait here, and not
aspect, since the latter keyword has a different and well-defined role within OSMO
and MODA.
In the last part of this section, we look into more detail at the viso-am branch, which
was designed considering Molecular Dynamics, Molecular Mechanics, Dissipative
Particle Dynamics and Monte Carlo methods. First of all, our choice to treat together
the atomistic and mesoscopic models is motivated by the fact that in many cases
they rely on the same numerical methods and a given software tool can address
both. Also, the meaning of “mesoscopic” within RoMM is different from the usual
acceptation: as soon as two or more atoms are grouped into an entity, this is considered
a mesoscopic model; since united-atom models already fall into this class, treating
these two granularity levels jointly seems well justified.
It is important to underline that the RoMM [30] classification principle is based
on what a modelling entity represents , a criterion that is indeed well suited to multiscale modelling. A complementary and quite natural classification could be based on
the mathematical nature of the modelling entity: for example, the classical models
could be distinguished in particle-based and field-based ones. While as a rule of
thumb AM models are particle-based and CO models are field-based, typically there
are also fields in AM models, discrete particles in CO and classical particles in EL
ones. Above all, it is important to realize that the two classifications are fundamentally
different: to give an extreme example, we could have a particle-based model of the
solar system, where each particle represents a planet!
In this direction, an important concept in VISO is that of viso:model_object
5
(cf. Fig. 4.2) which is the type of object entering the model and carrying degrees
of freedom. To be able to encompass different chemical objects, we need to adopt
a neutral vocabulary; in the AM branch, we choose to use viso-am:interaction_site
to indicate a point which is involved in (experiences) some interaction; it can represent the centre of a physical particle (an atom, a coarse-grained bead), but also be
a fictitious particle. Similarly, a viso-am:connected_object, where connectedness is
via bonds of some type, could be a molecule (in the chemical sense) or an aggregate. Finally, we have viso-am:interaction_surface, which is a surface affecting the
interactions and is treated as continuum, not as a collection of sites; for example, it
could be a wall. It is clear that our approach focuses on the mathematical nature of
5 Not to be confused with the “Object model” concept of Chap. 2.