init
Settings for the WESTPA configuration file.
__all__ = ['SystemConfig', 'PropagationConfig', 'ExecutableConfig', 'DataConfig', 'WestpaConfigConfig']
¶
DataConfig
¶
Bases: BaseModel
aux_compression_threshold = Field(default=1048576)
¶
The threshold in bytes for compressing the auxiliary data in a dataset on an iteration-by-iteration basis.
data_refs = Field(default_factory=DataRefs)
¶
References to various data paths.
datasets = Field(default=None)
¶
List of all datasets to load.
iter_prec = Field(default=8)
¶
The length of the iteration index with zero-padding. For the default value, iteration 1 would be specified as iter_00000001.
load_auxdata = Field(default=False)
¶
Load all datasets without an explicit load specification.
west_data_file = Field(default='west.h5')
¶
The name of the main HDF5 data storage file for the WESTPA simulation.
ExecutableConfig
¶
Bases: BaseModel
datasets = Field(default=[DatasetsConfig(name='pocket_rmsd'), DatasetsConfig(name='pocket_volume'), DatasetsConfig(name='backbone_rmsd'), DatasetsConfig(name='pocket_rog'), DatasetsConfig(name='pocket_jd')])
¶
gen_istate = Field(default=ExeChildConfig(enabled=True, executable='$WEST_SIM_ROOT/westpa_scripts/gen_istate.sh', stdout='/dev/null', stderr='$WEST_SIM_ROOT/job_logs/gen_istate.log'))
¶
Executable to generate initial state.
get_pcoord = Field(default=ExeChildConfig(enabled=True, executable='$WEST_SIM_ROOT/westpa_scripts/get_pcoord.sh', stdout='/dev/null', stderr='$WEST_SIM_ROOT/job_logs/get_pcoord.log'))
¶
Executable to get progress coordinate.
post_iteration = Field(default=ExeChildConfig(enabled=True, executable='$WEST_SIM_ROOT/westpa_scripts/post_iter.sh', stderr='$WEST_SIM_ROOT/job_logs/post_iter.log'))
¶
Post-iteration executable settings.
pre_iteration = Field(default=ExeChildConfig(enabled=False, executable='$WEST_SIM_ROOT/westpa_scripts/pre_iter.sh', stderr='$WEST_SIM_ROOT/job_logs/pre_iter.log'))
¶
Pre-iteration executable settings.
PropagationConfig
¶
Bases: BaseModel
Propagation settings for WESTPA.
block_size = Field(default=1)
¶
An integer defining how many segments should be passed to a worker at a time. When using the serial work manager, this value should be set to the maximum number of segments per iteration to avoid significant overhead incurred by the locking mechanism in the WMFutures framework. Parallel work managers might benefit from setting this value greater than one in some instances to decrease network communication load.
gen_istates = Field(default=True)
¶
Boolean specifying whether to generate initial states from the basis states.
The executable propagator defines a specific configuration block, and custom
propagators should override the WESTPropagator.gen_istate() method.
max_run_wallclock = None
¶
A time in dd:hh:mm:ss or hh:mm:ss specifying the maximum wallclock time of a particular WESTPA run. If running on a batch queuing system, this time should be set to less than the job allocation time to ensure that WESTPA shuts down cleanly.
max_total_iterations = None
¶
Max number of iterations to run.
save_transition_matrices = True
¶
Save transition matrices.
SystemConfig
¶
Bases: BaseModel
System settings for WESTPA.
WestpaConfigConfig
¶
Bases: BaseModel, Render
Configuration class for wrapping WESTPA configuration options. These options are scattered across a variety of sources shown below. We do our best to aggregate and explain each parameter.
data = Field(default_factory=DataConfig)
¶
Specify what, and how, data should be stored.
executable = Field(default_factory=ExecutableConfig)
¶
Provides information for the executable.
propagation = Field(default_factory=PropagationConfig)
¶
How to propagate the simulations.
system = Field(default_factory=SystemConfig)
¶
Configuration options for the physical systems we are simulating.