EMMO...EMMC Workshop on Interoperability in Materials Modelling, 7- 8 November 2017, Cambridge (UK) EMMO the EUROPEAN MATERIALS MODELLING ONTOLOGY Emanuele Ghedini (University of Bologna)

EMMC Workshop on Interoperability in Materials Modelling, 7-8 November 2017, Cambridge (UK)

EMMOthe EUROPEAN MATERIALS MODELLING ONTOLOGY

Emanuele Ghedini (University of Bologna)Adham Hashibon (Fraunhofer IWM)Jesper Friis (SINTEF)Gerhard Goldbeck (Goldbeck Consulting)Georg Schmitz (ACCESS)Anne de Baas (European Commission)


EMMO SCOPE

THEORETI-CIANS

EXPERIMEN-TALISTS

ACADEMIA

SOFTWARE HOUSES

INDUSTRIALEND USERS

SOFTWARE DEVELOPERS

MATERIALEXPERTS

INTERACTIONS BETWEEN MATERIALS MODELLING STAKEHOLDERS IS OFTEN THWARTED BY COMPLEXITY.

OFTEN THE MODELLING APPROACH IS ONLY PARTIALLY DESCRIBED, MENTIONING ONLY:

• PHENOMENA (e.g. microkinetics)• SCALE (e.g. atomic, mesoscale)• SOFTWARE (e.g. LAMMPS, OpenFOAM)• SOLVER (e.g. FEM, CV)

EACH COMMUNITY HAS ITS OWN TERMINOLOGY

MULTI-SCALE MATERIALS MODELLING REQUIRES MULTIDISCLIPLINARITY AND INTERACTIONS BETWEEN DIFFERENT MODELS

ESTABLISH A COMMON TERMINOLOGY (DEFINITION OF CONCEPTS AND VOCABULARY) IN MATERIALS MODELLING WHICH WILL LEAD TO

GREATLY SIMPLIFIED AND MUCH MORE EFFICIENT COMMUNICATION

SOLUTION


EMMO SCOPE

CEN/WS MODA

Materials modelling -terminology, classification and

metadata

RoMMReview of Materials Modelling VI

Anne de Baas, ECCEN Workshop Agreement

Endorsed by >15 EU organisation EMMC - MODA template

EMMOEUROPEAN MATERIALS MODELLING ONTOLOGY


EMMO SCOPE

EMMO MUST COVER ALL THE ASPECTS OF MATERIALS MODELLING:

• THE MATERIAL ITSELF THAT MUST BE DESCRIBED IN A RIGOROUS (ONTOLOGICAL) WAY

• THE PHYSICS LAW THAT DESCRIBES THE MATERIAL BEHAVIOUR

• THE PHYSICAL MODEL WHICH IS AN APPROXIMATION OF PHYSICS LAWS

• THE SOLVER INCLUDING THE NUMERICAL DISCRETIZATION METHOD THAT LEADS TO A SOLVABLE MATHEMATICAL REPRESENTATION UNDER CERTAIN SIMPLIFYING ASSUMPTIONS

• THE NUMERICAL SOLVER WHO PERFORMS THE CALCULATIONS

• THE POST PROCESSING OF DATA

MATERIALS MODELLING

MATERIAL USER CASE

PHYSICS LAW

PHYSICAL MODEL

SOLVER

POST-PROCESSING


BFO HIERARCHY

EMMO RELIES ON THE STRUCTURE OF THE BASIC FORMAL ONTOLOGY (BFO).

BFO is a genuine upper ontology. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.

The theory behind BFO was developed in 2002 first by Barry Smith and Pierre Grenon.

http://basic-formal-ontology.org/

The Basic Formal Ontology (BFO) is a small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains.

NOTE: Material Entity is any Independent Continuant that has some portion of matter as part (e.g. ‘human being’)

Hence: Materials Entity not same as Material


EMMO MATERIAL ENTITY BRANCH REQUIREMENTS

BEFORE TALKING ABOUT MODELLING IT SHOULD BE CLEAR WHAT WE WANT TO MODEL:

THE USER CASEUSER CASE

MATERIALSYSTEMPROCESS…

A robust, flexible and multi-perspectiveontological framework for representing materials is required to provide a univocal, complete description of the User Case.

ONE USER CASE, MULTIPLE MODELS

USER CASE

MODEL 1

MODEL 2

MODEL 3

Since materials are perceived at different scales, the Material Entities should cover all granularity levels, so that the same entity can be seen as a black box or as a collection of sub-parts. e.g. a molecule seen as a rigid body

the same molecule seen as collection of atoms

1

2


EMMO MATERIAL ENTITY BRANCH REQUIREMENTS

EMMO ADDRESSES THE ABOVEMENTIONED REQUIREMENTS MAKING USE OF THESE APPROACHES AND CONCEPTS TO DESCRIBE

WHAT WE WANT TO MODEL:

MEREOLOGY OBJECT AGGREGATE

x1

x2

x3

x4 ≡ yx5

OBJECT

the study of parts and the wholes they form

a causally united set of material entities

collections of not causally united objects


EMMO MEREOLOGY

He atom has_direct_parts:- electron_1- electron_2- He nucleus

n = 3

He nucleus has_direct_parts:- neutron_1- neutron_2- proton_1- proton_2

n = 4

He atom has_proper_parts:- electron_1- electron_2- neutron_1- neutron_2- proton_1- proton_2

n = 6

He atom has_direct_parts:- electron_1- electron_2- He nucleus

n = 3

Direct parthood gives (and retains) information about the entities that constitutes the direct lower granularity level.Atom does not inheres the nucleus direct parthood relations due to the lack of transitivity.

EMMO DIRECT PARTHOOD LETS US CREATE AHIERARCHY OF OBJECTS WITH DIFFERENT GRANULARITIES

Proper parthood gives information about all proper parts of an entity at all levels of granularity (granularity is flattened).Atom inheres the nucleus proper parthood relations due to transitivity.

AXIOMS

IMPLICATIONS ON ATOM


EMMO MEREOLOGY

EMMO BASIC MATERIAL ENTITIES BRANCH IS BUILD UPON A HIERARCHY OF MEREOLOGICAL RELATIONSSUCH AS:

is_part_of

is_proper_part_of

reflexive

transitive

antisymmetric

transitiveproper parthood

is_direct_part_of

antisymmetrictransitivereflexive

x ≡ x xy

z

x = y

x1

x2

x3

x4 ≡ yx5

only x3 is properparthood of y

properparthood

By dropping transitivity is_direct_part_ofidentifies the entity proper parts that are at the very next lower granularity level

e.g.: nucleus is_direct_part_of atomproton is_direct_part_of nucleus

proper parthood

x y

y x

xy

z

y is_direct_part_of xz is_direct_part_of y

z is not direct part of x


BFO OBJECT

OBJECTb is an object means: - b is a material entity which manifests a causal unity CUn of some type- b is of a type instances of which are maximal relative to CUn.

To say that b is maximal relative to some criterion of causal unity CUn means:- b is causally unified relative to CUn at t- if for some t and c (b is_continuant_part_of c at t & c is causally unified relative to the same CUn) then b and c are identical (i.e. an atom cannot have atoms as parts)

We still need to define the Material Entities (BFO) (Materials, Devices, Products etc) in a rigorous way:We achieve that in EMMO by representing things that are the subjects of investigations by using the BFO concept of Object

• An Object can be defined only if related to a particular Causal Unity

• We can define Causal Unity criteria depending on our perspective (e.g. Physics, Medicine)

• BFO proposes three Causal Unity criteria

• EMMO will formalise other Causal Unity criteria coming from physics/materials science.


BFO OBJECT CAUSAL UNITY

CU 1 : Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering.

CU 2 : Causal unity via internal physical forcesHere the material parts of a material entity are combined together causally by sufficiently strong physical forces strong enough to act in such a way as to hold the object together relative to the strength of attractive or destructive forces in its ordinary environmental neighbourhood.

CU 3 : Causal unity via engineered assembly of componentsHere the material parts of a material entity are combined together via mechanical assemblies joined for example through screws or other fasteners.

THE THREE BFO PROPOSED CUs ARE:


EMMO MEREOLOGY

e-

pn

has_part

EMMO Material Entities are defined by a Hierarchy of parthood relations,

combining the concepts of direct parthood and object

With EMMO we create a representation of the real world granularity of Material Entities that follows physics and materials science perspectives.

A User Case Material can be described univocally by declaring Entities under EMMOhierarchy.

The basic idea is that the material can be represented at different levels of granularity, depending on perspective.

has_part

has_part has_part has_part has_part has_part


EMMO MATERIAL BRANCH (FIRST LEVELS)

ONE REALITY WITH FOUR VERIDICAL VIEWSAT DIFFERENT LEVELS OF GRANULARITY

THE EMMO MATERIAL BRANCH EXTENDS THE BFOMATERIAL ENTITY WITH MATERIAL OBJECTS AT 4 DIFFERENT LEVELS OF GRANULARITY.

The engineered-material co-incides with aggregates of material objects (simulated or observed)


BFO OBJECT AGGREGATE

A User Case Material may consist of not causally related parts. We can thus not describe it as Object.We need a way to describe collections of n>1 Objects (e.G. Atoms in molecule)

MEMBERSHIP PARTHOODb is_member_part_of c at t = Def.- b is an object- c is an object aggregate- there is at t a mutually exhaustive and pairwise disjoint partition of c into objectsx1,..., xn (for some n > 1) with b = xi for some 1 ≤ i ≤ n.

OBJECT AGGREGATEb is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as is_member_part_of b at all times at which b exists.

is_member_part_of

is_part_ofantisymmetric

transitivereflexive

is_member_part_of is not transitive

AN OBJECT AGGREGATE IS DISJOINT WITH OBJECT (i.e. it has no causal unity)

AN AGGREGATE PARTITIONING MAY NOT BE UNIQUE, SINCE IT CAN CREATE MEMBERSHIP RELATIONS ACROSS MORE THAN ONE GRANULARITY LEVEL

x1

x2

x3

x6x4

x5

x1

x2

x3

x7x4 x5

x6

A1 = (x1, x2, x3, x4, x5, x6) A2 = (x1, x2, x3, x7)


EMMO OBJECT AGGREGATE USE AND GRANULARITY LEVELS

car (object)

piston (object)

steel ring (object) grain aggregate

mechanical parts aggregate

car components aggregate

molecule (object) atoms aggregate

In EMMO the same material or product can havetwo different material entity representations : The ‘Object’ coincides with an ‘Object Aggregate’

The ‘Object Aggregate’ members can be at different levels of granularity;e.g. Steel ring can be seen as grain aggregate, atom aggregate of electron aggregate.


EMMO MATERIAL BRANCH (FIRST LEVELS)

THE EMMO MATERIAL BRANCH EXTENDS THE BFOMATERIAL BRANCH BY TAKING INTO ACCOUNT THE RoMM ENTITY CATEGORIZATION

ONE REALITY WITH FOUR VERIDICAL VIEWSAT DIFFERENT LEVELS OF GRANULARITY


EMMO MATERIAL BRANCH (FULL LEVELS)

THE EMMO MATERIAL BRANCH INCREASES THE LEVEL OF DETAILS OF THE RoMM ENTITIES BY INTRODUCING PHYSICS BASED OBJECT DEFINITIONS (e.g. photon, nanostructure, solid)


EMMO MATERIAL BRANCH

has_direct_part

has_member_part

THE EMMO PROVIDES ALSO AN UNDERLYING DIRECT PARTHOOD AND PROPER PARTHOOD AXIOMATIC RELATION STRUCTURE THAT REFLECTS THE SEVERAL LEVEL OF GRANULARITY OF MATERIALS.

• axiomatic means that the depicted relations must occur for each particular class of entities

• only few samples of the axiomatic EMMO intra-entities relations are shown here

• however other parthood relations between individuals may occur if no restrictions have been declared (e.g. system_1 is_direct_part_of system_2)


EMMO MEREOLOGICAL BASIS

fluid

elementary

nucleon atom composite

scale/number of partsmolecule

no parts has parts

hν

e-

n

p

system

nucleus

subatomic atomistic mesoscopic_object

nanostructure

continuum_object

solid component

engineered_object

grain

engineered_material

systemcomponent

THE EMMO MATERIAL CLASSES AMBITION IS TO COVER ALL THE PHYSICS AND MATERIAL SCIENCE SCALES.


EMMO N2 MOLECULE EXAMPLE

has_individual

is_a

has_individual

has_direct_part

is_a

is_a

is_a

is_a

is_ais_a

is_a

is_ais_ais_a

is_a

has_direct_part

EXAMPLE OF MULTIPLE object AND

object_aggregateREPRESENTATION OF

A N2 MOLECULE


ROMM MODEL TYPES

RoMM VI

FOUR TYPES OFPHYSICS BASED MODELS


aggregate of meso objects

EMMO MEREOLOGY FOR OBSERVATIONS AND SIMULATIONS

e-

e-

ATOMISTIC OBSERVATIONS AND MODELS

MESOSCOPIC OBSERVATIONS AND MODELS

CONTINUUM OBSERVATIONS AND MODELS

electron and nucleus objects

aggregate of electrons and nuclei



ELECTRONIC OBSERVATIONS AND MODELS

atom objects aggregate of atoms aggregate of atoms

meso objects

continuum objects

EACH material can be observed at different levels of granularity and can be modelled by different granularities.

ONE USER CASE:MULTIPLE OBSERVATION GRANULARITY

LEVELS MULTIPLE MODEL GRANULARITY LEVELS


EMMO EXAMPLE ON PLASMA NANOPARTICLE SYNTHESIS REACTOR

EXAMPLE OF EMMO REPRESENTATION OF A MATERIAL PROCESSING SYSTEM

PLASMA NANOPARTICLE SYNTHESIS REACTOR

NANODOMENanomaterials via Gas-Phase Synthesis:

A Design-Oriented Modelling andEngineering Approach



PLASMA REACTORsystem

ICP TORCHsystem, component

COILcomponent

CONFINEMENT TUBEcomponent

REACTOR VESSELcomponent, solid_object

PROBEcomponent

PROCESSING GAS EULERIANfluid_object

CHAMBERsite

Ar ATOM 1atom_object

Si ATOM 1atom_object

Si NANOPARTICLES EULERIAN

continuum_object

Si NANOPARTICLES LAGRANGIAN

meso_aggregate

PROCESSING GAS LAGRANGIANatom_aggregate

has_direct_part

has_member_part



Ar ATOM natom_object

Si ATOM matom_object

…

…

Si NANOPARTICLE 1nano_structure


Si NANOPARTICLE pnano_structure

…



Si ATOM qatom_object

…

Si NUCLEUS inucleus_object

ELECTRON jnucleus_object

Si MICROPARTICLESLAGRANGIAN

object_aggregate

Si MICROPARTICLE 1solid_object


Si MICROPARTICLE rsolid_object

…





COILcomponent



PROBEcomponent


CHAMBERsite




continuum_object


meso_aggregate


has_direct_part

has_member_part





…

…




…




…




object_aggregate




…

MATERIAL USER CASE





COILcomponent



PROBEcomponent


CHAMBERsite




continuum_object


meso_aggregate






…

…




…




…




object_aggregate




…

ELECTRONIC MODEL

has_direct_part

has_member_part





COILcomponent



PROBEcomponent


CHAMBERsite




continuum_object


meso_aggregate






…

…




…




…




object_aggregate




…

ATOMISTIC MODEL

has_direct_part

has_member_part





COILcomponent



PROBEcomponent


CHAMBERsite




continuum_object


meso_aggregate






…

…




…




…




object_aggregate




…

MESOSCOPIC MODEL

has_direct_part

has_member_part





COILcomponent



PROBEcomponent


CHAMBERsite




continuum_object


meso_aggregate






…

…




…




…




object_aggregate




…

CONTINUUM MODEL

has_direct_part

has_member_part



ONE USER CASE, MULTIPLE MODELS

• the choice of the model to apply for a particular part of the user case is done by the modeller

• more than one approach can be used for the same component

• this approach facilitate multi scale approach

One ontology to rule them all.

MATERIAL USER CASE

PHYSICAL MODELS


EMMO MODEL AND PHYSICAL PROPERTIES

THE GENERICALLY DEPENDENT CONTINUANT BRANCH WILL INCLUDE ALL THE CLASSES THAT DEFINES PHYSICAL LAWS AND MODELS

THE EMMO MATERIAL ENTITY BRANCH FUNDAMENTALS HAVE ALREADY BEEN SETTLED AS SHOWN IN PREVIOUS SLIDES

THE SPECIFICALLY DEPENDENT CONTINUANT BRANCH INCLUDES ALL THE CLASSES THAT DEFINES THE PHYSICAL PROPERTIES OF MATERIAL ENTITIES

THE IMMATERIAL ENTITY BRANCH FOR EMMO IS STILL TO BE DEVELOPED


physical_propertyA quality that is univocally measurable by each observer by a measuring process, and that can be used to describe a state of a physical system.

physical_quantityA physical_property of a phenomenon, body, or continuum object, that can be quantified with respect to a standardized reference material_entityinstance (e.g. the prototype meter bar, the kg prototype).

EMMO MODEL AND PHYSICAL PROPERTIES


PHYSICAL QUANTITY

MATERIAL ENTITY

SDC GDCIC

PHYSICAL VARIABLE

PHYSICAL PARAMETER

PHYSICSEQUATION

MATERIAL RELATION

MODEL

PHYSICAL LAW

MATERIAL LAWMEASUREMENT PROCESS

has_quality

s-depends_on

has_participant

MODELLING ENTITY

has_part

is_model_for

is_model_for

is_model_for

EMMO APPROACH ON MODELLING


CONCLUSIONS AND OUTLOOK

ACHIEVEMENTS• CLARIFIED THE MEREOLOGICAL STRUCTURE IN BFO AND INTRODUCED A NEW RELATION is_direct_part_of TO PRESERVE

GRANULARITY

• PROVIDED A DOUBLE REPRESENTATION OF MATERIALS VIA object AND object_aggregate SUITABLE FOR A MODELLING PERSPECTIVE

• CREATION OF A BFO COMPLIANT MATERIAL REPRESENTATION FOR USER CASE MATERIAL THAT SPANS OVER GRANULARITY LEVELS

• DEFINED THE NEED FOR MORE CAUSAL UNITIES TO INTEGRATE THE PHYSICIST/MATERIAL SCIENTIST PERSPECTIVE INTO object

NEXT STEPS• DEVELOPMENT OF THE MODELLING, PHYSICAL PROPERTIES AND IMMATERIAL BRANCHES

• TEST AGAINST DOCUMENTED USER CASES (i.e. projects MODA)

• DEVELOPMENT OF CONSISTENT CLASS RELATIONS FOR A ROBUST OWL-DL IMPLEMENTATION, INCLUDING REASONER USE

OUTLOOK• EMMO WILL BE THE BASIS FOR INTEROPERABILITY SOFTWARE THAT REFLECTS ITS HIERARCHY AND RELATIONSHIPS, INCLUDING

FILE FORMATS (e.g. HDF5), SUITABLE FOR SOTWARE VENDORS IMPLEMENTATION IN EMMO, SIMILAR TO WHAT WAS DONE IN ALLOTROPE.


ACKNOWLEDGEMENTS

• Emanuele Ghedini acknowledges funding received from the European Union's Horizon 2020 research and innovation programme, for the NANODOME project, Grant Agreement No. XXX

• Adham Hashibon, Jesper Friis, Gerhard Goldbeck and Georg Schmitz acknowledge funding received from the European Union's Horizon 2020 research and innovation programme, for the EMMC-CSA project, Grant Agreement No. 723867.


EMMO MODELLING APPROACH (DRAFT)

NUCLEUS

ELECTRON 1

ELECTRON 2

POSITION

MASS

ATO

M

has_

prop

er_p

art

POSITION_PV

MASS_PVhas_

qual

ity

NEWTON EQUATION

FORCE_PV

MY FORCE FIELD EQUATION

material_entityphysical_quantity

physical_variable

physics_based_model

physics_equation

material_relation

ATOMISTIC MODEL OF

ATOM

has_

prop

er_p

art

has_

prop

er_p

art

parameter

MASS CALCULATOR

SDC GDCIC

unknown

NEWTON’S LAW OF MOTION

represents

physical_law

ATOMIC MASS TABLE

represents

material_law

MY FORCE FIELD

represents

modelling_entity

MASSMEASUREMENT

POSITIONMEASUREMENT

FORCEMEASUREMENT

process

s-depends_on

has_participant has_participanthas_participant

is_m

easu

re_f

or

represents

Documents

EMMO...EMMC Workshop on Interoperability in Materials Modelling, 7- 8 November 2017, Cambridge (UK) EMMO the EUROPEAN MATERIALS MODELLING ONTOLOGY Emanuele Ghedini (University of Bologna)