Environment
EnvVars
¶
Bases: BaseModel
SIM_NAME: str = Field(default='$(basename $WEST_SIM_ROOT)')
class-attribute
instance-attribute
¶
Simulation name
WEST_CURRENT_ITER: int = Field(ge=1, default=1)
class-attribute
instance-attribute
¶
Current iteration number
WEST_CURRENT_SEG_DATA_REF: str | None = Field(default=None)
class-attribute
instance-attribute
¶
General-purpose reference, based on current segment information, configured in west.cfg. Usually used for storage paths.
WEST_CURRENT_SEG_ID: int = Field(ge=0, default=0)
class-attribute
instance-attribute
¶
Current segment ID
WEST_PARENT_ID: int | None = Field(default=None)
class-attribute
instance-attribute
¶
Segment ID of parent segment. Negative for initial points.
WEST_PCOORD_RETURN: str | None = Field(default=None)
class-attribute
instance-attribute
¶
Where progress coordinate data must be stored.
WEST_PYTHON: str = Field(default='$(which python)')
class-attribute
instance-attribute
¶
path to python executable to run the WESTPA simulation
WEST_PYTHONPATH: str | None = Field(default=None)
class-attribute
instance-attribute
¶
path to any additional modules that WESTPA will require to run the simulation
WEST_SIM_ROOT: str = Field(default='$PWD')
class-attribute
instance-attribute
¶
path to the base directory containing the WESTPA install
WestpaEnv
¶
Bases: BaseModel
Configuration for WESTPA environment setup script; typically called env.sh.
This is used by
write_env_script
to create the env.sh script for setting up the WESTPA environment.
lines_append: MutableSequence[str] = Field(default=[])
class-attribute
instance-attribute
¶
Lines to append to the env.sh script.
lines_prepend: MutableSequence[str] = Field(default=[])
class-attribute
instance-attribute
¶
Lines to prepend to the env.sh script.
load_modules: MutableSequence[str] = Field(default=[])
class-attribute
instance-attribute
¶
List of modules to load before running WESTPA simulation.
Each module is loaded using module load command.
Warning
These modules are specific to the cluster and the software version and often need to be loaded in a specific order. Please consult the cluster documentation.
Example
If we were to use AMBER 22 for a WESTPA simulation on the University of Pittsburgh's H2P cluster, we would set this to
For NAMD 2.13, it would be
For GROMACS 2021.2 it would be
purge_modules: bool = Field(default=True)
class-attribute
instance-attribute
¶
If True, remove all loaded modules before loading the modules in load_modules.