Contexts
ContextValidator
¶
Base class for validating simulation contexts.
extra_anions(value, context)
staticmethod
¶
Validate extra_anions
extra_cations(value, context)
staticmethod
¶
Validate extra_cations
validate(context_manager)
classmethod
¶
Validate contexts for simulations.
| PARAMETER | DESCRIPTION |
|---|---|
context_manager |
A simulation context manager to validate.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
bool
|
If the context is valid. |
write(value, context)
staticmethod
¶
Validate write
SimulationContextManager(yaml_path=None, **kwargs)
¶
Contexts for setting up molecular simulations.
| PARAMETER | DESCRIPTION |
|---|---|
yaml_path |
Path to YAML file to load into the context.
TYPE:
|
anion_identity: str = 'Cl-'
instance-attribute
¶
Identity of the anion in the system.
cation_identity: str = 'Na+'
instance-attribute
¶
Identity of the cation in the system.
compute_platform: str = 'mpi'
instance-attribute
¶
Desired platform to run simulations on.
Options:
mpi: Message passing interface for central processing units (CPUs).cuda: Compute Unified Device Architecture (CUDA) for graphics processing units (GPUs).
coord_path: str | None = None
instance-attribute
¶
Path to coordinate file for current stage.
cpu_cores: int | None = None
instance-attribute
¶
Number of CPU cores to use if requested
extra_anions: int = 0
instance-attribute
¶
Number of extra anions to add to the system.
extra_cations: int = 0
instance-attribute
¶
Number of extra cations to add to the system.
ff_dna: str | None = None
instance-attribute
¶
Molecular mechanics force fields for DNA.
ff_glycam: str | None = None
instance-attribute
¶
Molecular mechanics force fields for sugars
ff_ions: str | None = None
instance-attribute
¶
Molecular mechanics force fields for ions.
ff_lipid: str | None = None
instance-attribute
¶
Molecular mechanics force fields for lipids.
ff_protein: str | None = None
instance-attribute
¶
Molecular mechanics force field used to describe polypeptides.
ff_rna: str | None = None
instance-attribute
¶
Molecular mechanics force fields for RNA.
ff_small_molecule: str | None = None
instance-attribute
¶
Molecular mechanics force fields for small molecules.
ff_water: str | None = None
instance-attribute
¶
Molecular mechanics force fields for water.
input_dir: str | None = None
instance-attribute
¶
Path to input directory for current stage.
input_kwargs: dict[str, Any] | None = None
instance-attribute
¶
Simulation keyword arguments for input files.
input_path: str | None = None
instance-attribute
¶
Path to input file for current stage.
neutralize_charge: bool = True
instance-attribute
¶
Flag to determine if system charge should be neutralized by placing additional ions.
output_dir: str | None = None
instance-attribute
¶
Path to output directory for current stage.
output_path: str | None = None
instance-attribute
¶
Path to output file for current stage.
prev_coordinate_path: str | None = None
instance-attribute
¶
Path to coordinate file of previous stage
prev_restart_path: str | None = None
instance-attribute
¶
Path to restart file from previous stage or initial coordinates.
ref_coord_path: str | None = None
instance-attribute
¶
Path to reference coordinate file. This is often used for enforcing restraints.
restart_path: str | None = None
instance-attribute
¶
Path to restart file for this stage.
run_path: str | None = None
instance-attribute
¶
Path to run file.
sbatch_options: dict[str, Any] | None = None
instance-attribute
¶
sbatch options
for a slurm submission script.
Some common options are:
job-name,
nodes,
ntasks-per-node,
cpus-per-task,
gpus,
gres,
cpus-per-gpu,
chdir,
output,
error,
time,
clusters,
partition,
account.
These options are written in the format of #SBATCH --{key}={value}.
scratch_dir: str | None = None
instance-attribute
¶
Specify path for scratch directory if desired. If None, we do not use
scratch.
slurm_lines: list[str] | None = None
instance-attribute
¶
Lines for a slurm submission script.
slurm_path: str | None = None
instance-attribute
¶
Path to slurm submission file.
solvent_ionic_strength: float = 0.15
instance-attribute
¶
Ionic strength of the solvent in mole/L.
solvent_padding: float = 10.0
instance-attribute
¶
Padding between solute and box edge to fill with solvent in Angstroms.
splits: int = 1
instance-attribute
¶
Split simulation stage into several chunks.
stage_name: str | None = None
instance-attribute
¶
Name or label for simulation stage.
stages: Collection[dict[str, Any]] | None = None
instance-attribute
¶
Contexts for successive stages. Stage \(i > 0\) is assumed to be restarted from stage \(i - 1\).
submit: bool = False
instance-attribute
¶
Submit the job.
system_charge: int = 0
instance-attribute
¶
Net charge of the molecular system.
topo_path: str | None = None
instance-attribute
¶
Path to topology file.
verbosity: int | str | None = None
instance-attribute
¶
Verbosity level for logging.
work_dir: str | None = None
instance-attribute
¶
Working directory for preparing calculations.
write: bool = False
instance-attribute
¶
Write files.
write_dir: str | None = None
instance-attribute
¶
Write directory.
yaml_path = yaml_path
instance-attribute
¶
Path of YAML file that was loaded. Defaults to None.
__enter__()
¶
Enter the context and return the current context as a dictionary.
__exit__(exc_type, exc_value, exc_tb)
¶
Exit the context.
| PARAMETER | DESCRIPTION |
|---|---|
exc_type |
Type of the exception.
|
exc_value |
Value of the exception.
|
exc_tb |
Traceback information.
|
from_yaml(yaml_path)
¶
Load context information from a YAML file. This will only update data contained in the YAML file.
| PARAMETER | DESCRIPTION |
|---|---|
yaml_path |
Path to YAML file to load.
TYPE:
|
get()
¶
cli_validate_yaml_context()
¶
Command-line interface for validating YAML context files.