pysages.methods.utils

Overview

pysages.methods.utils.HistogramLogger(period)

Implements a Callback functor for methods.

pysages.methods.utils.MetaDLogger(...)

Logs the state of the collective variable and other parameters in Metadynamics.

Details

Collection of helpful classes for methods.

This includes callback functor objects (callable classes).

class pysages.methods.utils.SerialExecutor

Subclass of concurrent.futures.Executor used as the default task manager. It will execute all tasks in serial.

submit(fn, *args, **kwargs)

Executes fn(*args, **kwargs) and returns a Future object wrapping the result.

class pysages.methods.utils.ReplicasConfiguration(copies: int = 1, executor=<pysages.methods.utils.SerialExecutor object>)

Stores the information necessary to execute multiple simulation runs, including the number of copies of the system and the task manager.

class pysages.methods.utils.HistogramLogger(period: int, offset: int = 0)

Implements a Callback functor for methods. Logs the state of the collective variable to generate histograms.

Parameters:

  • period – Time steps between logging of collective variables.

  • offset – Time steps at the beginning of a run used for equilibration.

get_histograms(**kwargs)

Helper function to generate histograms from the collected CV data. kwargs are passed on to numpy.histogramdd function.

get_means()

Returns mean values of the histogram data.

get_cov()

Returns covariance matrix of the histogram data.

reset()

Reset internal state.

class pysages.methods.utils.MetaDLogger(hills_file, log_period)

Logs the state of the collective variable and other parameters in Metadynamics.

Parameters:

  • hills_file – Name of the output hills log file.

  • log_period – Time steps between logging of collective variables and Metadynamics parameters.

save_hills(xi, sigma, height)

Append the centers, standard deviations and heights to log file.

pysages.methods.utils.listify(arg, replicas, name, dtype)

Returns a list of with length replicas of arg if arg is not a list, or arg if it is already a list of length replicas.

pysages.methods.utils.numpyfy_vals(dictionary: dict, numpy_only: bool = False)

Iterate all keys of the dictionary and convert every possible value into a numpy array. We recommend to pickle final analyzed results are numpyfying with numpy_only=True to avoid pickling issues.

Strings and numpy arrays, that would result in dtype == object are not converted.

Parameters:

  • dictionary (dict) – Input dictionary, which keys are attempted to be converted to numpy arrays.

  • numpy_only (bool) – If true, any not simple numpy array object is excluded from the results.

Returns:

dict

Return type:

The same dictionary, but keys are preferably numpy arrays.