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: \(\lfloor\sqrt\text{size}\rfloor\))

  • args.separation (number) – minimal separation of samples for time averages in sampling steps (default: size)

  • 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.