Blocking Scheme¶
- class halmd.observables.dynamics.blocking_scheme(args)¶
Construct blocking scheme.
Parameters: - args – keyword arguments
- args.max_lag (number) – maximum lag time in MD units
- args.every (number) – sampling interval of lowest coarse-graining level in integration steps
- args.size (number) – size of each block, determines coarse-graining factor
- args.shift (number) – coarse-graining shift between odd and even levels
(default:
)
- args.separation (number) – minimal separation of samples for time
averages in sampling steps (default: –
)
- args.flush (number) – interval in seconds for flushing the accumulated results to the file (default: 900)
- disconnect()¶
Disconnect blocking scheme from sampler.
- class correlation(args)¶
Compute time correlation function.
Parameters: - args (table) – keyword arguments
- args.tcf – time correlation function
- args.file – instance of halmd.io.writers.h5md
- args.location (string table) – location within file (optional)
The argument tcf specifies the time correlation function. It is expected to provide the attributes acquire (1 or 2 callables that yield the samples to be correlated) and desc (module description) as well as a method writer (file writer). Suitable modules are found in halmd.observables.dynamics, see there for details.
The argument location specifies a path in a structured file format like H5MD given as a table of strings. If omitted it is defined by the time correlation function, typically {"dynamics", particle group, name of correlation function}.
- disconnect()¶
Disconnect correlation function from blocking scheme.