Environment

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

WestpaEnvVars

Bases: BaseModel

SIM_NAME = Field(default='$(basename $WEST_SIM_ROOT)')

Simulation name

WEST_CURRENT_ITER = Field(ge=1, default=1)

Current iteration number

WEST_CURRENT_SEG_DATA_REF = Field(default=None)

General-purpose reference, based on current segment information, configured in west.cfg. Usually used for storage paths.

WEST_CURRENT_SEG_ID = Field(ge=0, default=0)

Current segment ID

WEST_PARENT_ID = Field(default=None)

Segment ID of parent segment. Negative for initial points.

WEST_PCOORD_RETURN = Field(default=None)

Where progress coordinate data must be stored.

WEST_PYTHON = Field(default='$(which python)')

path to python executable to run the WESTPA simulation

WEST_PYTHONPATH = Field(default=None)

path to any additional modules that WESTPA will require to run the simulation

WEST_SIM_ROOT = Field(default='$PWD')

path to the base directory containing the WESTPA install