MC¶

class poreana.mc.MC¶

This class contains the Monte Carlo part of the diffusion calculation. The class initializes the MC (Monte Carlo) and contains all functions to execute the MC cycle part of the diffusion calculation.

The MC calculation can be started with run().

Methods

`__class__`	alias of `type`
`__delattr__`(name, /)	Implement delattr(self, name).
`__dict__`
`__dir__`(/)	Default dir() implementation.
`__doc__`
`__eq__`(value, /)	Return self==value.
`__format__`(format_spec, /)	Default object formatter.
`__ge__`(value, /)	Return self>=value.
`__getattribute__`(name, /)	Return getattr(self, name).
`__gt__`(value, /)	Return self>value.
`__hash__`(/)	Return hash(self).
`__init__`()
`__init_subclass__`	This method is called when a class is subclassed.
`__le__`(value, /)	Return self<=value.
`__lt__`(value, /)	Return self<value.
`__module__`
`__ne__`(value, /)	Return self!=value.
`__new__`(args, *kwargs)
`__reduce__`(/)	Helper for pickle.
`__reduce_ex__`(protocol, /)	Helper for pickle.
`__repr__`(/)	Return repr(self).
`__setattr__`(name, value, /)	Implement setattr(self, name, value).
`__sizeof__`(/)	Size of object in memory, in bytes.
`__str__`(/)	Return str(self).
`__subclasshook__`	Abstract classes can override this to customize issubclass().
`__weakref__`	list of weak references to the object (if defined)
`_init_rate_matrix_pbc`(bin_num, diff_bin, df_bin)	This function estimates the rate Matrix R for the current free energy and log diffusion profiles over the bins for periodic boundary conditions.
`_init_stats`(model)	This function sets the MC statistic counters to zero after every MC run.
`_log_likelihood_z`(model[, temp])	This function estimate the likelihood of the current free energy or diffusion profile over the bins in a simulation box.
`_mcmove_df`(model)	This function does the MC move for the free energy profile and adjust the coefficents of the model.
`_mcmove_diffusion`(model)	This function does the MC move for the diffusion profile and adjust one coefficient of the model.
`_run_helper`(model, len_step, do_radial)	Helper function for MC run
`_update_movewidth_mc`(imc[, radial])	This function sets a new MC move width after a define number of MC steps \(n_\text{MC,update}\).
`run`(model, link_out[, nmc_eq, nmc, ...])	This function do the MC Cycle to calculate the diffusion and free energy profile over the bins and save the results in an output hdf5 file.