Class: Barostat¶

Settings used for the simulation barostat.

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

         classDiagram
    class Barostat
    click Barostat href "../../classes/Barostat/"
      Barostat : barostat_algorithm
        
          
    
        
        
        Barostat --> "0..1" BarostatAlgorithm : barostat_algorithm
        click BarostatAlgorithm href "../../enums/BarostatAlgorithm/"
    

        
      Barostat : compressibility
        
          
    
        
        
        Barostat --> "0..1" CompressibilityQuantity : compressibility
        click CompressibilityQuantity href "../../classes/CompressibilityQuantity/"
    

        
      Barostat : compressibility_vector
        
          
    
        
        
        Barostat --> "0..1" MatrixCompressibilityQuantity : compressibility_vector
        click MatrixCompressibilityQuantity href "../../classes/MatrixCompressibilityQuantity/"
    

        
      Barostat : pressure_coupling_frequency
        
      Barostat : pressure_coupling_type
        
          
    
        
        
        Barostat --> "0..1" PressureCouplingType : pressure_coupling_type
        click PressureCouplingType href "../../enums/PressureCouplingType/"
    

        
      Barostat : pressure_time_constant
        
          
    
        
        
        Barostat --> "0..1" TimeQuantity : pressure_time_constant
        click TimeQuantity href "../../classes/TimeQuantity/"
    

        
      Barostat : target_pressure
        
          
    
        
        
        Barostat --> "0..1" PressureQuantity : target_pressure
        click PressureQuantity href "../../classes/PressureQuantity/"
    

        
      Barostat : target_pressure_vector
        
          
    
        
        
        Barostat --> "0..1" MatrixPressureQuantity : target_pressure_vector
        click MatrixPressureQuantity href "../../classes/MatrixPressureQuantity/"

Slots¶

Name	Cardinality and Range	Description	Inheritance
barostat_algorithm	0..1 BarostatAlgorithm	List of barostat algorithms used in the simulation	direct
compressibility	0..1 CompressibilityQuantity	Compressibility of the simulated system, given as a float	direct
compressibility_vector	0..1 MatrixCompressibilityQuantity	Compressibility of the simulated system, given as a float	direct
target_pressure	0..1 PressureQuantity	Target/reference pressure set to reach in the simulation, given as a float	direct
target_pressure_vector	0..1 MatrixPressureQuantity	Target/reference pressure set to reach in the simulation, given as a 3x3 arra…	direct
pressure_time_constant	0..1 TimeQuantity	Time constant/step (relaxation time of pressure) used for coupling the system…	direct
pressure_coupling_frequency	0..1 integer	Step frequency to apply the barostat, given as an integer	direct
pressure_coupling_type	0..1 PressureCouplingType	List of coupling types for adjusting box vectors	direct

Usages¶

used by	used in	type	used
SimulationSettings	barostat	range	Barostat

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/Barostat
native	https://CCPBioSim.ac.uk/biosim-schema/Barostat

LinkML Source¶

Direct¶

name: Barostat
description: Settings used for the simulation barostat.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- barostat_algorithm
- compressibility
- compressibility_vector
- target_pressure
- target_pressure_vector
- pressure_time_constant
- pressure_coupling_frequency
- pressure_coupling_type

Induced¶

name: Barostat
description: Settings used for the simulation barostat.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  barostat_algorithm:
    name: barostat_algorithm
    description: List of barostat algorithms used in the simulation.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: BarostatAlgorithm
  compressibility:
    name: compressibility
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: comp
          unit: 1e10-6 1/bar
    description: Compressibility of the simulated system, given as a float.
    examples:
    - value: 44.6 1e10-6 1/bar
    - value: 4.5e-5 1/bar
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: CompressibilityQuantity
  compressibility_vector:
    name: compressibility_vector
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: compressibility
          unit: 1/bar
    description: Compressibility of the simulated system, given as a float.
    examples:
    - value: 44.6 1e10-6 1/bar
    - value: 4.5e-5 1/bar
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: MatrixCompressibilityQuantity
  target_pressure:
    name: target_pressure
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: pres0
          unit: bar
    description: Target/reference pressure set to reach in the simulation, given as
      a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: PressureQuantity
  target_pressure_vector:
    name: target_pressure_vector
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: ref-p
          unit: bar
    description: Target/reference pressure set to reach in the simulation, given as
      a 3x3 array.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: MatrixPressureQuantity
  pressure_time_constant:
    name: pressure_time_constant
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: tau-p
          unit: ps
        - engine: amber
          key: taup
          unit: ps
    description: Time constant/step (relaxation time of pressure) used for coupling
      the system pressure, given as a float.
    examples:
    - value: 1.0 ps
    - value: 5.0 ps
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: TimeQuantity
  pressure_coupling_frequency:
    name: pressure_coupling_frequency
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: nstpcouple
    description: Step frequency to apply the barostat, given as an integer.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: integer
  pressure_coupling_type:
    name: pressure_coupling_type
    description: List of coupling types for adjusting box vectors.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Barostat
    domain_of:
    - Barostat
    range: PressureCouplingType