OSMO: Ontology for Simulation, Modelling, and Optimization
Virtual Materials Marketplace (VIMMP) project consortium
GNU Lesser General Public License (LGPL) version 3
Martin Thomas Horsch (ORCID 0000-0002-9464-6739)
Silvia Chiacchiera (ORCID 0000-0003-0422-7870)
Gianluca Boccardo (ORCID 0000-0003-1264-8237)
Vladimir Lobaskin (ORCID 0000-0002-5231-0639)
materials model classifier, i.e., a symbol for categories of materials-model related entities, following RoMM (note: these are descriptors, not identical with the described entities)
granularity level (from RoMM), i.e., electronic, atomistic, mesoscopic, or continuum level according to RoMM
granularity level label: electronic materials modelling
granularity level label: atomistic materials modelling
granularity level label: mesoscopic materials modelling
granularity level label: continuum materials modelling
physical equation type, i.e., a symbol referring to the physical equation underlying a model, mostly following RoMM (n.b., these entities are not models, they are descriptors of models)
electronic physical equation type, i.e., a PE type at the electronic granularity level
PE type EL.1: Ab-initio quantum mechanical (or first principle) model
RoMM model vocabulary category 1.1, OSMO PE type EL.1
PE type EL.2: Electronic many-body and/or effective Hamiltonian model
RoMM model vocabulary category 1.2, OSMO PE type EL.2
PE type EL.3: QM model of the response to time-dependent fields
RoMM model vocabulary category 1.3, OSMO PE type EL.3
PE type EL.4: Statistical charge transport model
RoMM model vocabulary category 1.4, OSMO PE type EL.4
PE type EL.5: Statistical electron spin transport model
RoMM model vocabulary category 1.5, OSMO PE type EL.5
atomistic physical equation type, i.e., a PE type that at the atomistic granularity level
PE type A.1: Classical-mechanical density functional theory (atomistic)
RoMM model vocabulary category 2.1, OSMO PE type A.1
PE type A.2: Molecular statics (atomistic), energy minimization
RoMM model vocabulary category 2.2, OSMO PE type A.2
PE type A.3: Molecular dynamics (atomistic)
RoMM model vocabulary category 2.3, OSMO PE type A.3
PE type A.4: Partition function (atomistic), e.g., for a Monte Carlo solver
RoMM model vocabulary category 2.4, OSMO PE type A.4
RoMM model vocabulary category 2.5, OSMO PE type A.5
PE type A.6: Statistical transport model (atomistic)
RoMM model vocabulary categories 2.6 and 2.7, OSMO PE type A.6
mesoscopic physical equation type, i.e., a PE type at the mesoscopic granularity level
PE type M.1: Classical-mechanical density functional theory (mesoscopic)
RoMM model vocabulary category 3.1, OSMO PE type M.1
PE type M.2: Molecular statics (mesoscopic), i.e., energy minimization
PE type M.3: Molecular dynamics (mesoscopic), i.e., coarse-grained or united-atom modelling
RoMM model vocabulary category 3.2, OSMO PE type M.3
PE type M.4: Partition function (mesoscopic), e.g., for a Monte Carlo solver
RoMM model vocabulary category 3.3, OSMO PE type M.4
RoMM model vocabulary category 3.4, OSMO PE type M.5
PE type M.6: Statistical transport model (mesoscopic)
RoMM model vocabulary categories 3.5, OSMO PE type M.6
continuum physical equation type, i.e., a PE type that operates at the continuum granularity level
RoMM model vocabulary category 4.1, OSMO PE type CO.1
RoMM model vocabulary category 4.2, OSMO PE type CO.2
PE type CO.3: Continuum modelling of heat transfer and thermomechanics
RoMM model vocabulary category 4.3, OSMO PE type CO.3
PE type CO.4: Phase field model or continuum density gradient theory
RoMM model vocabulary category 4.4.2, OSMO PE type CO.4
RoMM model vocabulary category 4.4.1, OSMO PE type CO.5
PE type CO.6: Continuum modelling of chemical reaction kinetics
RoMM model vocabulary category 4.5, OSMO PE type CO.6
PE type CO.7: Continuum electromagnetism model (including optics, magnetism, etc.)
RoMM model vocabulary category 4.6, OSMO PE type CO.7
PE type CO.8: Continuum process model (including devices and components of chemical/mechanical processes, flow-chart models, etc.)
RoMM model vocabulary category 4.7, OSMO PE type CO.8
workflow resource, i.e., a workflow entity that can be contained as a node-like element or as a subgraph by a workflow graph
label to be used, e.g., in graph representations and for other visualization purposes
virtual graph, i.e., a workflow graph that is variably instantiated based on workflow-dependent quantities; e.g., a virtual graph might be instantiated multiple times in parallel or sequentially, or the way in which it is instantiated might qualitatively depend on input parameters in a significant way, going beyond the conventional role of an input parameter (n.b., virtual graphs do not contain anything; instead, they are instantiated by concrete graphs that contain further elements)
contingent graph, i.e., a virtual graph that is only present/active if one or multiple conditions are fulfilled
whenever one or several conditions are not fulfilled, a resource that is contingent on them is absent/inactive
indexed graph, i.e., a virtual graph that is instantiated multiple times, with an index
indicates whether any of the multiple instantiations of this resource are coupled (synchronized) with each other
indicates whether any of the multiple instantiations of this resource are sequentially linked to each other
points to the logical variable/index to which multiple values are assigned
unit in which the index values are given (not required; in many typical cases, the index is dimensionless)
points to each of the multiple values that are given to the index
section, i.e., a simulation overview, application case, model, solver, or processor (as in MODA)
points to information that plays a role within the respective OSMO/MODA section
points to a format employed for I/O in the technical implementation of the respective OSMO/MODA section
points to information that needs to be provided
points to information required or produced by a OSMO/MODA section
points to information that is obtained as a result from the respective OSMO/MODA section
points to required physical (thermodynamic or mechanical) information, which needs to be provided, e.g., from the output of another OSMO/MODA section
points to physical information that plays a role within the respective OSMO/MODA section
points to desired physical (thermodynamic or mechanical) information which is obtained as a result from the respective OSMO/MODA section
points to an aspect associated with the respective OSMO/MODA section
points to the workflow (sub)graph to which a particular use case or materials model applies
section aspect, i.e., a descriptor of an application case, model, solver, or processor that can be represented by a section
plain-text description of an aspect/subsection (as in MODA)
numerical value associated with an aspect/subsection (as in MODA)
points to an object associated with an aspect/subsection
points to an annotation object (i.e., a non-paradigmatic object) associated with an aspect/subsection
points to a paradigmatic object associated with an aspect/subsection
boundary condition, i.e., any given information that needs to be taken into account
error statement, i.e., an aspect that contains an accuracy assertion
geometry information, i.e., geometry considered by an OSMO/MODA section
material information, i.e., aspect related to the material considered by an OSMO/MODA section
points to the element function associated with the present material information (an OSMO/MODA section can have multiple material informations, describing different units)
method type, i.e., type and/or name information on a method employed by an OSMO/MODA section
parameter aspect, i.e., an aspect characterizing a parameter associated with an OSMO/MODA section
section description, i.e., any descriptive-type information concerning an OSMO/MODA section
section literature, i.e., a literature reference associated with an OSMO/MODA section
software, i.e., an executable numerical artefact
temporal discretization, i.e., temporal discretization approach conceptually underlying an OSMO/MODA section
time span information, i.e., statement on the time interval considered, modelled, or represented by an OSMO/MODA section
points to an aspect of a simulation overview (following MODA)
Simulation overview aspect, i.e., an aspect of a simulation overview (as specified in the MODA cover page)
General description of the use case (MODA cover page, aspect 1), to be provided as plain-text content
General description of the chain of models (MODA cover page, aspect 2), to be provided as plain-text content; n.b., the detailed workflow and specification of how exactly the models are connected should be provided in terms of OSMO/LDT workflow notation. Here, it is appropriate to provide only a summary in text form.
publication that documents data pertaining to the present simulation workflow (MODA cover page, aspect 3)
Access conditions - MODA cover page, aspect 4: Please list whether the model and/or data are free, commercial or open source. Please list the owner and the name of the software or database (including web link if available).
Rationale - MODA cover page, aspect 5: Please give a textual rationale of why you as a modeller have chosen these models and this workflow. This should include the reason why a particular aspect of the user case is to be simulated with a particular model.
application case, i.e., a scenario, point of view, or subjective or negotiated set of aims
points to an application-case aspect (as in MODA or extensions of MODA)
plain-text summary of the application case
points to a materials modelling project that addresses the present application case
points to information on the application decision support system
plain-text summary of the MODA/OSMO use case
points to a use-case aspect (as in MODA)
points to information on the use-case decision support system (UDSS)
application-case aspect (similar as in MODA or extensions of MODA)
information on the decision support system
use-case description (MODA subsection 1.1), describes aspects of a use case textually
use-case material information (MODA subsection 1.2), characterizes/describes the considered material
use-case geometry information (MODA subsection 1.3), characterizes/describes the considered system geometry
use-case time span (MODA subsection 1.4), characterizes/describes the considered time interval
use-case boundary condition (MODA subsection 1.5), characterizes/describes a thermodynamic, spatio-temporal, or any other boundary condition
use-case literature (MODA subsection 1.6), cites a reference that is relevant or of interest for the use case
information on the use-case decision support system (UDSS)
points to an aspect associated with a materials model (as in MODA)
model aspect, i.e., an aspect of a materials model
model type (MODA subsection 2.1), characterizes/describes the model type or class or the approach to modelling that is followed
model granularity aspect (MODA subsection 2.2), characterizes the RoMM granularity level of a model
governing equation (GE) as defined by RoMM, i.e., a physical equation (PE) or materials relation (MR)
physical equation (PE) as defined by RoMM, cf. MODA subsection 2.3
materials relation (MR) as defined by RoMM, cf. MODA subsection 2.4
model boundary condition (MODA subsection 2.5), characterizes/describes a boundary condition that is applied to the model
model error statement, characterizes/describes the error or uncertainty associated with a model
points to an aspect associated with a solver
MODA solver aspect, i.e., an aspect of a solver (similar to MODA)
solver method type (MODA subsection 3.1), characterizes/describes the name and type of the solver
solver software (MODA subsection 3.2), characterizes/describes a code/package to be used as a solver
solver time step (MODA subsection 3.3), numerical time step employed by the solver
solver computational representation (MODA subsection 3.4), characterizes/describes how the solver numerically represents the model and/or the material
solver CR of the model, i.e., a computational representation of (all or part of) the governing equations of the employed materials model
solver CR of PE, i.e., a computational representation specifically of one or multiple physical equations (PE)
solver CR of MR, i.e., a computational representation specifically of one or multiple materials relations (MR)
solver CR of the material, i.e., a computational representation of the considered use case or material
solver CR of the material, i.e., a computational representation that combines model and material (or use case) aspects
solver boundary condition (MODA subsection 3.5), characterizes/describes a computational boundary condition of a solver
solver parameter (MODA subsection 3.6), i.e., a parameter of a solver
solver error statement, characterizes/describes the error or uncertainty associated with a solver output
processor (like a MODA postprocessor, however, without implying execution subsequent to a solver, which would correspond to the special case represented by the subclass osmo:postprocessor)
points to an aspect associated with a processor
OSMO-only subsection 4.4, extending MODA
preprocessor, i.e., a processor that operates before a solver or during solver initialization
coupled processor, i.e., a processor that is synchronized with a solver and operates on the fly
postprocessor, i.e., a processor that operates subsequent to a solver or during solver finalization
data processor, i.e., a processor that is not coupled or immediately linked to a solver
processor aspect, i.e., an aspect of a processor (as in MODA)
processor method type (MODA subsection 4.2), characterizes/describes the methodology employed by a processor
preprocessor method type, i.e., a method type associated with a preprocessor
coupled processor method type, i.e., a method type associated with a coupled processor
postprocessor method type, i.e., a method type associated with a postprocessor
trajectory analyser, i.e., a postprocessor that analyses simulation trajectory output
data processor method type, i.e., a method type associated with a data processor
processor error statement (MODA subsection 4.3), characterizes/describes the error or uncertainty associated with a processor output
processor software (OSMO aspect 4.4, extending MODA), characterizes/describes a code/package to be used as a processor
workflow graph, i.e., a model, a simulation workflow, or a composition of constituent elements and aspects thereof that can be represented in logical data transfer (LDT) notation
points to the use case or materials model considered by a workflow (sub)graph
points to the materials model considered by a workflow (sub)graph
points to the use case considered by a workflow (sub)graph
points to the overview of a simulation workflow
points to a subgraph, i.e., a graph that is subordinate (to the present graph) by containment and/or instantiation
points to the position, or a position, where the workflow execution begins
points to the position, or a position, where the workflow execution terminates
[G has_cause F] means that in every execution, F needs to finish before G can begin
if [F is_coupled_with G] they must occur synchronously when a workflow that contains them is executed
if [F is direct cause of G] there is an immediate link by which G depends on the conclusion of F
two workflow graphs F and G are independent if they (and any of their subgraphs) are not coupled or linked to each other
if [F is linked to G] they cannot be executed concurrently; one side depends on the completion of the other side
[F is_contained_within G] if F is contained within graph G, e.g., as a subgraph
workflow node, i.e., a workflow graph that contains exactly one workflow resource
logical node, i.e., a workflow node that contains exactly one logical resource
simulation workflow, i.e., a (complete) workflow graph of an actually executable simulation workflow
Use-case 'name', to be provided as part of an overall simulation workflow description, cf. heading of the MODA cover sheet ('MOdelling DAta providing a description for <user-case name> simulated in project ')
Project acronym, to be provided as part of an overall simulation workflow description, cf. heading of the MODA cover sheet ('MOdelling DAta providing a description for <user-case name> simulated in project ')
Data owner, information to be provided as part of an overall simulation workflow description, cf. heading of the MODA cover sheet; since conducting the simulation requires the authorization and hence 'occurrence' of a/the data owner, this relation is positioned below viprs:has_requirement_satisfied_by
URL of a diagram ('workflow picture' according to the MODA cover sheet) illustrating the simulation workflow
points to a node that contains a logical resource with (all or part of) the end outcome of the simulation workflow
concrete graph, i.e., a workflow graph that is a concrete (non-virtual) workflow resource
[G contains R] if R occurs as a proper part/component of graph G
use of this relation: a virtual graph can be defined by describing a concrete graph that instantiates it (e.g., a single loop iteration), i.e., which is related to the corresponding virtual graph by osmo:instantiates
physical variable, i.e., a logical variable defined in terms of a material property
unique physical constant, i.e., a physical variable with a unique constant value
condition, i.e., a statement concerning values of properties and/or parameters and/or their relation to each other
points to a parameter (e.g., variable or input value) occurring in a condition
points to a parameter that is determined before workflow execution begins, i.e., an input parameter that is not specified by the user
points to a parameter that is computed within the workflow, but available and fixed at run time (of the element associate with the present condition), i.e., an input parameter that is not specified by the user
points to a parameter that is only determined at run time (of the element associate with the present condition) or that is varied at run time
points to a parameter for which no value can be obtained (in an executable simulation workflow, undetermined parameters can only be present in conditions associated with elements that are never executed)
qualitative condition, i.e., a condition (e.g., an inequality) that compares or connects properties and/or parameters without imposing any particular value for any of them, even if the values of all the others are given
quantitative condition, i.e., a condition (e.g., an equation) that imposes a particular value for one of the considered quantities assuming that all others are given
logical resource, i.e., a notational element of a simulation workflow to which data (i.e., logical variables) are formally written and/or from where they can be formally read
points to the logical resource ID (LRID) associated with the present logical resource; n.b., this ID has technical purposes (for notational and visualization purposes, use osmo:has_logical_label)
states whether an external entity (user interaction, or some process not represented in the workflow) has write access to this resource at execution time
logical term, i.e., a logical variable or a value that can be assigned to a logical variable
identifies a term by a non-negative integer number; in particular, use for array terms (numbering convention: from 0 to array size minus 1)
elementary term, i.e., a logical term without any internal structure
unit associated with any assigned decimal values
structure term, i.e., a logical term with an internal structure
logical value, i.e., an entity that can be assigned to a logical variable as its value
elementary value, i.e., an entity that can be assigned to an elementary logical (variable) as its value
structure value, i.e., an entity that can be assigned to a logical structure as its value
logical variable, i.e., a term that can be exchanged by interaction with logical resources
points to a value associated with a logical variable
value associated with a logical variable at any concrete state/point in time, either explictly specified or clear from context
value to be associated with a logical variable in the absence of any other overriding assertion
value associated with a logical variable in an initial state, e.g., at the start of a workflow or subworkflow execution
value associated with a logical variable in a terminal state, e.g., at the end of a workflow or subworkflow execution
identifies a variable by a non-negative integer number; in particular, use for logical arrays (numbering convention: from 0 to array size minus 1)
format by which the present logical variable is represented in the technical implementation of a simulation workflow
logical constant, i.e., a logical variable with constant value
elementary logical, i.e., a logical variable that does not contain any (sub-)variables as structure elements
value associated with an elementary logical variable
value associated with an elementary logical variable in a terminal state, e.g., at the end of a workflow or subworkflow execution
logical structure, i.e., a logical variable that contains (sub-)variables as structure elements
logical array, i.e., a unique structure with indexed elements (n.b., for indexing, use has_variable_index, starting from 0)
points to a variable that contains the (dynamic) array size; convention: element indices run from 0 to the array size minus one
unit in which values of array elements are given (does not apply if the array elements are logical structures)
points to the generic representation of the array elements (which is the same for all index values)
this property can be used to assign a variable name to the array index
points to one particular array element (identified by a specific index value)
value that gives the array size; convention: element indices run from 0 to the array size minus one
logical scalar, i.e., an logical variable that can have only one value at the same time
logical collection, i.e., a logical variable that can carry multiple values (e.g., representing a set, map, list, or array)
logical access, i.e., a notational process/connection by which an OSMO/MODA section accesses a logical resource
logical read access, i.e., a notational process/connection by which an OSMO/MODA section reads from a logical resource
logical write access, i.e., a notational process/connection by which an OSMO/MODA section writes to a logical resource
points to the Chemical Abstracts Service Registry Number (CASRN, or CAS number) associated with a material
points to the EC number (i.e., the European common market number) associated with a material
CAS listed material, i.e., a material that has a Chemical Abstracts Service Registry Number (CASRN, or CAS number)
EC listed material, i.e., a material that has an EC number and is traded on the European common market
EINECS listed material, i.e., an EC listed material from the European Inventory of Existing Commercial Chemical Substances (EINECS)
ELINCS listed material, i.e., an EC listed material from the European List of Notified Chemical Substances (ELINCS)
NLP listed material, i.e., an EC listed material from the No-Longer-Polymers (NLP) List
Unit function, i.e., purpose or impact of one out of multiple coexisting units of the same or similar type
optimization objective, i.e., a logical variable that is employed as a criterion during optimization
maximization objective, i.e., a target quantity that is to be maximized
minimization objective, i.e., a target quantity that is to be minimized
decision support system, i.e., a data and software infrastructure that facilitates decision support
points to a constraint of the optimization problem
points to a target quantity that is to be maximized
points to a target quantity that is to be minimized
application decision support system, i.e., a decision support system that occurs in an application case
use-case decision support system (UDSS), i.e., a decision support system that is applied to a use case
PE_TYPE_A.1
PE_TYPE_A.2
PE_TYPE_A.3
PE_TYPE_A.4
PE_TYPE_A.5
PE_TYPE_A.6
PE_TYPE_CO.1
PE_TYPE_CO.2
PE_TYPE_CO.3
PE_TYPE_CO.4
PE_TYPE_CO.5
PE_TYPE_CO.6
PE_TYPE_CO.7
PE_TYPE_CO.8
PE_TYPE_EL.1
PE_TYPE_EL.2
PE_TYPE_EL.3
PE_TYPE_EL.4
PE_TYPE_EL.5
PE_TYPE_M.1
PE_TYPE_M.2
PE_TYPE_M.3
PE_TYPE_M.4
PE_TYPE_M.5
PE_TYPE_M.6