Contexts
simulation.contexts.RenderingConfig
¶
Bases: BaseModel, YamlIO
Configuration for rendering files to write.
dir_input: str = '.'
class-attribute
instance-attribute
¶
Path to a directory relative to
dir_work that will contain
input files.
dir_output: str = '.'
class-attribute
instance-attribute
¶
Path to a directory relative to
dir_work that the simulation will
store output files.
dir_work: str = '.'
class-attribute
instance-attribute
¶
Working directory to write files.
simulation.contexts.RuntimeConfig
¶
Bases: BaseModel, YamlIO
Configuration options during the simulation runtime.
dir_input: str = '.'
class-attribute
instance-attribute
¶
Path to a directory relative to
dir_work that will contain
input files.
dir_output: str = '.'
class-attribute
instance-attribute
¶
Path to a directory relative to
dir_work that the simulation will
store output files.
dir_run: str = '.'
class-attribute
instance-attribute
¶
Directory that calculations are performed in. This can be the same as
dir_work
or some scratch space like $SLURM_SCRATCH.
dir_work: str = '.'
class-attribute
instance-attribute
¶
Working directory during runtime. This can be the current work directory or
a workload manager directory such as $SLURM_SUBMIT_DIR.
splits: int = 1
class-attribute
instance-attribute
¶
Split simulation stage into several chunks.
simulation.contexts.SimlifyConfig
¶
Bases: BaseModel, YamlIO
Contexts for setting up molecular simulations.
engine: Any = None
class-attribute
instance-attribute
¶
Atomea workflow schema for the molecular simulation engine (e.g.,
Amber22Schema).
extra_lines_topo_gen: Iterable[str] | None = None
class-attribute
instance-attribute
¶
Extra lines to include when generating a topology.
label: str | None = None
class-attribute
instance-attribute
¶
Label for this specific simulation.
rendering: RenderingConfig = Field(default_factory=RenderingConfig)
class-attribute
instance-attribute
¶
runtime: RuntimeConfig = Field(default_factory=RuntimeConfig)
class-attribute
instance-attribute
¶
slurm: SlurmSchema = Field(default_factory=SlurmSchema)
class-attribute
instance-attribute
¶
solution: SolutionConfig = Field(default_factory=SolutionConfig)
class-attribute
instance-attribute
¶
temp: dict[str, Any] = Field(default={}, exclude=True)
class-attribute
instance-attribute
¶
topology: TopologyConfig = Field(default_factory=TopologyConfig)
class-attribute
instance-attribute
¶
simulation.contexts.SolutionConfig
¶
Bases: BaseModel, YamlIO
charge_anion_extra: int = 0
class-attribute
instance-attribute
¶
Number of extra anions of type [charge_anion_identity][simulation.contexts.SimlifyConfig.charge_anion_identity] to add to
the system. This does not include any ions added if [charge_neutralize][simulation.contexts.SimlifyConfig.charge_neutralize] is True.
charge_anion_identity: str = 'Cl-'
class-attribute
instance-attribute
¶
Many simulations include anions to either neutralize charge or prepare the solvent environment to have a specific ionic concentration. This specifies the anion to add to accomplish this.
charge_cation_extra: int = 0
class-attribute
instance-attribute
¶
Number of extra cations of type [charge_cation_identity][simulation.contexts.SimlifyConfig.charge_cation_identity] to add to the
system. This does not include any ions added if [charge_neutralize][simulation.contexts.SimlifyConfig.charge_neutralize] is True.
charge_cation_identity: str = 'Na+'
class-attribute
instance-attribute
¶
Many simulations include cations to either neutralize charge or prepare the solvent environment to have a specific ionic concentration. This specifies the cation to add to accomplish this.
charge_net: int = 0
class-attribute
instance-attribute
¶
Net charge of the molecular system before any preparation.
charge_neutralize: bool = True
class-attribute
instance-attribute
¶
Flag to determine if system charge should be neutralized by placing
additional ions of type [charge_cation_identity][simulation.contexts.SimlifyConfig.charge_cation_identity]
or [charge_anion_identity][simulation.contexts.SimlifyConfig.charge_anion_identity] based on
the value of [charge_net][simulation.contexts.SimlifyConfig.charge_net].
solvent_ionic_strength: float = 0.15
class-attribute
instance-attribute
¶
Ionic strength of the solvent in mol/L.
solvent_padding: float = 10.0
class-attribute
instance-attribute
¶
Padding between solute and box edge to fill with solvent in Angstroms.