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simphony / simphony-metadata

[LEGACY] This repository contains the metadata definitions used in SimPhoNy project.
BSD 2-Clause "Simplified" License
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Meaning of variables in unclear and unspecified #82

Closed stefanoborini closed 7 years ago

stefanoborini commented 7 years ago

The variables entry is unclear in its use and purpose

307 LENNARD_JONES_6_12: 308 parent: CUBA.PAIR_POTENTIAL 309 definition: A Lennard-Jones 6-12 Potential 310 models: [CUBA.ATOMISTIC] 311 variables: [CUBA.POSITION, CUBA.POTENTIAL_ENERGY] 312 CUBA.CUTOFF_DISTANCE: 313 default: 1.0 314 CUBA.ENERGY_WELL_DEPTH: 315 default: 1.0 316 CUBA.VAN_DER_WAALS_RADIUS: 317 default: 1.0

ahashibon commented 7 years ago

These are meant to give more information and metadata on the equation. The variables correspond to the MODA template and aim at giving extra semantic knowledge on the equation defined and assist in giving meanning to them. Moreover, the collection of all variables in a CUDS indicate which variables should be expected and supported on the PARTICLES, MESH and LATTICE entities. Currently, they provide a way to query which variables are supprted by an equation (ME, PE, etc).

stefanoborini commented 7 years ago

@ahashibon Ok so briefly said it's the information needed somewhere else for the lennard jones entity to make sense. Correct?

ahashibon commented 7 years ago

yes! and this information should be carried/provided by each entity (here LJ) itself!

stefanoborini commented 7 years ago

Ok, I am getting conflicting information. Should be carried by the Lennard Jones object or should be carried somewhere else?

ahashibon commented 7 years ago

@stefano: The information itself is "stored" on the entity itself (in the VARIABLE entry), but will be utilised by wrappers or validators of CUDS! This is what I mean by "carried" the entity carry this information about itself as part of its own metadata.

stefanoborini commented 7 years ago

@ahashibon How do you envision this concept to be converted into a python object?

ahashibon commented 7 years ago

now, for engine wrappers, simply that we can query this information on any entity hat has it. For visualisation wrappers for example would be able to use this information to prepare GUI, or to allocate space etc.

stefanoborini commented 7 years ago

I assume that with "this information" you mean the list, not the actual value of position and potential energy. In other words, is the current object layout found in simphony/cuds/meta/lennard_jones_6_12.py what you would expect?

ahashibon commented 7 years ago

yes!

stefanoborini commented 7 years ago

The meaning has been extracted and rendered in the file specs. Closing.