Extension for conceptual dictionary

[aazocar]

Most of the needed terminology is focused on the subclasses of:

• Physical Quantity,
• Calculated property,
• Input Parameter or
• Output Parameter

Here we collect the classes to be added. Hierarchy for the properties will be discussed at a later point.

@srmnitc please add here

[aazocar]

• Related to DFT (VASP) jobs:

Superclass	Label	Definition	Comment
Calculated property	Total Energy
Calculated property	Total Magnetic Moment
Physical Quantity	SimulationCellLength		change to PQ
Physical Quantity	Pressure
Physical Quantity	Volume
Output Parameter	Number of ionic steps
Input Parameter	Energy Cutoff
Input Parameter	KPoint Mesh
KPoint Mesh	KPoint Mesh		Explicit k-point mesh
KPoint Mesh	KPoint Mesh		Gamma-centered mesh
KPoint Mesh	KPoint Mesh		Monkhorst-Pack mesh

[aazocar]

• Related to MD (LAMMPS) jobs:

Superclass	Label	Definition	Comment
Physical Property	Temperature		Used as InputParameter currently
Physical Property	Pressure		Used as InputParameter currently
Physical Property	Volume		Used as ComputedProperty currently
Physical Property/CP	Kinetic Energy
Physical Property/CP	Potential Energy
Physical Quantity	SimulationCellLength		change to PQ
Physical Property/CP	Total Energy
PhysicalQuantity	Time
Input Parameter	TimeStep
Time	Simulation Time

[aazocar]

• Related to EOS jobs:

Superclass	Label	Definition	Comment
Input Parameter	Volume range
CalculatedProperty/PQ	TotalEnergy		currently labelled EquilibriumEnergy
CalculatedProperty	BulkModulus
PhysicalProperty	Volume		currently labelled EquilibriumVolume

also simulation cell lengths as before..

[srmnitc]

• Related to QuasiHarmonic jobs:

Superclass	Label	Definition	Comment
CalculatedProperty	FreeEnergy		currently labelled QuasiHarmonicFreeEnergy
PhysicalProperty	Temperature		currently labelled QuasiHarmonicTemperature
PhysicalProperty	Volume		currently labelled QuasiHarmonicVolume

also simulation cell lengths as before..

[srmnitc]

• Related to ThermodynamicIntegration jobs:

Superclass	Label	Definition	Comment
CalculatedProperty	FreeEnergy
PhysicalProperty	Temperature
PhysicalProperty	Volume		currently labelled AtomicVolume since its vol/atom

also simulation cell lengths as before..

[srmnitc]

Further considerations

For LAMMPS:

• [Discussion] A major category we are missing are thermostats/barostats. We should consider if we want to add somethings like hasThermostat -> Langevin etc, and same for Barostat. Or simply use InputParameter.
• [NoTermNeeded] Force Tolerance, Energy tolerance etc for minimization - should be instantiated as needed using InputParameter.
• [NoTermNeeded] Initial, final, and averaged temperature, pressure, energy - covered by above definitions, instance can be used and labelled as needed.
• [NoTermNeeded] Force norm - should be ideally a per-atom quantity; otherwise it would be averaged force, max force etc which could be covered by OutputParameter
• [Discussion] MinimizationAlgorithm - Algo used in minimization, eg: conjugate gradient, full list here

For VASP:

• [ToDo] Import remaining XC functionals from MDO

General:

• PBC

[srmnitc]

@Tara-Lakshmipathy @pkruzikova After going through the OpenBis data model, this is the proposed update to the ontology. There are still some points to be discussed. If you have any suggestions or comments, please feel free to add here!

[srmnitc]

MASS?

[Tara-Lakshmipathy]

Did we agree on a strategy for periodic boundaries?

[srmnitc]

An additional, PeriodicBoundaryConditions -> PeriodicityinXdirection , similarly for Y and Z will be added.

[aazocar]

Ok, this is the schematic for the new classes. I'll go ahead with the changes now.