Class: Integrator¶

Settings used for the simulation integrator.

URI: https://CCPBioSim.ac.uk/biosim-schema/Integrator

         classDiagram
    class Integrator
    click Integrator href "../../classes/Integrator/"
      Integrator : frame_step
        
          
    
        
        
        Integrator --> "0..1" TimeQuantity : frame_step
        click TimeQuantity href "../../classes/TimeQuantity/"
    

        
      Integrator : integrator_algorithm
        
          
    
        
        
        Integrator --> "0..1" IntegratorAlgorithm : integrator_algorithm
        click IntegratorAlgorithm href "../../enums/IntegratorAlgorithm/"
    

        
      Integrator : number_of_steps
        
      Integrator : simulation_time
        
          
    
        
        
        Integrator --> "0..1" TimeQuantity : simulation_time
        click TimeQuantity href "../../classes/TimeQuantity/"
    

        
      Integrator : time_step
        
          
    
        
        
        Integrator --> "0..1" TimeQuantity : time_step
        click TimeQuantity href "../../classes/TimeQuantity/"

Slots¶

Name	Cardinality and Range	Description	Inheritance
integrator_algorithm	0..1 IntegratorAlgorithm	List of integrator algorithms used to integrate the simulation	direct
frame_step	0..1 TimeQuantity	Time between saved snapshots/frames in a simulation, given as a float	direct
time_step	0..1 TimeQuantity	Time between integration steps in a simulation, given as a float	direct
number_of_steps	0..1 integer	Number of integration steps performed in the simulation, given as an integer	direct
simulation_time	0..1 TimeQuantity	Total time molecular dynamics have been sampled in a simulation trajectory, o…	direct

Usages¶

used by	used in	type	used
SimulationSettings	integrator	range	Integrator

Identifier and Mapping Information¶

Schema Source¶

from schema: https://CCPBioSim.ac.uk/biosim-schema/

Mappings¶

Mapping Type	Mapped Value
self	https://CCPBioSim.ac.uk/biosim-schema/Integrator
native	https://CCPBioSim.ac.uk/biosim-schema/Integrator

LinkML Source¶

Direct¶

name: Integrator
description: Settings used for the simulation integrator.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- integrator_algorithm
- frame_step
- time_step
- number_of_steps
- simulation_time

Induced¶

name: Integrator
description: Settings used for the simulation integrator.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  integrator_algorithm:
    name: integrator_algorithm
    description: List of integrator algorithms used to integrate the simulation.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: IntegratorAlgorithm
  frame_step:
    name: frame_step
    description: Time between saved snapshots/frames in a simulation, given as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: TimeQuantity
  time_step:
    name: time_step
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: dt
          unit: ps
        - engine: gromacs
          key: dt
          unit: ps
        - engine: lammps
          key: timestep
          unit: fs
    description: Time between integration steps in a simulation, given as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    aliases:
    - Integration Step
    - Time Step
    - dT
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: TimeQuantity
  number_of_steps:
    name: number_of_steps
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: nstlim
        - engine: gromacs
          key: nsteps
    description: Number of integration steps performed in the simulation, given as
      an integer.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: integer
  simulation_time:
    name: simulation_time
    description: Total time molecular dynamics have been sampled in a simulation trajectory,
      often given by the number of integration steps multiplied by the simulation
      time step used by the integrator, given as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: TimeQuantity