Skip to content

init

__all__ = ['WestpaConfig', 'WestpaEnv']

WestpaConfig

Bases: BaseModel, YamlIO

The root configuration for west.cfg files.

env = Field(default_factory=WestpaEnv)

west = Field(default_factory=WestpaConfigConfig)

WestpaEnv

Bases: BaseModel

Configuration for WESTPA environment setup script; typically called env.sh.

This is used by [write_env_script][setup.westpa.scripts.write_env_script] to create the env.sh script for setting up the WESTPA environment.

lines_append = Field(default=[])

Lines to append to the env.sh script.

lines_prepend = Field(default=[])

Lines to prepend to the env.sh script.

load_modules = Field(default=[])

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

load_modules = ["gcc/10.2.0", "openmpi/4.1.1", "amber/22"]

For NAMD 2.13, it would be

load_modules = ["intel/2018.2.199", "openmpi/2.1.1", "namd/3.1.1"]

For GROMACS 2021.2 it would be

load_modules = ["gcc/10.2.0", "openmpi/4.1.1", "gromacs/2021.2"]

purge_modules = Field(default=True)

If True, remove all loaded modules before loading the modules in load_modules.

vars = Field(default_factory=WestpaEnvVars)

Keys and values for the environment variables to be set in the env.sh script.

Additional environment variables can be added with the following syntax:

WestpaConfig.env.vars.KEY = VALUE

For example, setting the number of processors (NPROCS) to 12 would be

WestpaConfig.env.vars.NPROCS = 12